Data from: Spring ephemeral Erythronium umbilicatum may not be vulnerable to phenological mismatch with overstory trees

https://doi.org/10.5061/dryad.0k6djhbc9

In this study, we aimed to understand the effects of experimental shade on the spring ephemeral Erythronium umbilicatum and predict the extent of phenological mismatch between E. umbilicatum and the canopy under future climate warming. We conducted this study in the Duke Forest (southeastern North Carolina, USA). We experimentally shaded Erythronium umbilicatum for one to six additional weeks prior to canopy leaf-out to test for immediate and lagged effects of early shading on the timing of senescence and the probability of survival and flowering. To predict the potential for earlier shading, we combined long-term time series of spring air temperature (PRISM Climate Group, Oregon State University, 2022), remotely-sensed tree leaf-out (MOD13Q1.061; Didan, 2021), and E. umbilicatum flowering phenology.

File: modisveg_sub.csv

Description: Data used to evaluate the day of year that canopy closed each year. Raw data were downloaded from the remotely-sensed MODIS Terra enhanced vegetation index (EVI) timeseries from 2000 to 2024 at each site (MOD13Q1.061; Didan, 2021).

Variables

• year: year satellite image was taken (2000-2024)
• catyear: year as a categorical variable
• site: site where measurement was taken, (G24 or ONA)
• doy: Julian day of year that the observation was made
• normevi: normalized EVI data within each year (EVInormalized = (EVI - EVImin) / (EVImax - EVImin), where EVImin is the minimum EVI value recorded at a site in a given year, and EVImax is the maximum EVI value

File: pendant.data.csv

Description: Data collected from in-situ HOBO Pendant data loggers (Onset, HOBO UA-002-64 Pendant Light and Temperature Data Logger). We monitored light intensity (Lux) and soil surface temperature by deploying a pair of HOBO Pendant data loggers in four shade plots and one sham plot at ONA. We placed the Pendants on top of the soil and leaf litter, with the light sensors facing upwards. Each pair consisted of a Pendant in the middle of the plot and one southwest of the plot, just outside the covered area. The Pendants recorded data every 10 minutes from March 28 - April 4, 2023.

Variables

• date-time: date and time of measurement
• hour: hour of day measurement was taken, rounded down
• plot: name of plot where the measurement was taken
• treatment.location: the treatment and location at the point of each measurement, (shade inside, shade outside, sham inside, sham outside)
• treatment: treatment of the plot, (shade or sham)
• location: location of Pendant within plot, (inside or outside)
• lux: Pendant measurement of light level (lux)
• log.lux: log of the lux measurement (log lux)
• temp: Pendant measurement of temperature (°C)

File: prism.all.csv

Description: Monthly temperature data from PRISM (PRISM Climate Group, Oregon State University, 2022) and average temperatures of select combinations of consecutive months, weighted by the number of days in each month. Monthly data are 4 km resolution PRISM temperature data for January through April from each observation year at each site.

Variables:

• site: site where measurement was taken, (G24 or ONA)
• year: year measurement was taken, (1970-2024)
• jan: mean January temperature from specified site and year (°C)
• feb: mean February temperature from specified site and year (°C)
• march: mean March temperature from specified site and year (°C)
• april: mean April temperature from specified site and year (°C)
• temp1: mean of January and February temperature, weighted by the number of days in each month (°C)
• temp2: mean January, February and March temperature, weighted by the number of days in each month (°C)
• temp3: mean February and March temperature, weighted by the number of days in each month (°C)
• temp4: mean February, March, and April temperature, weighted by the number of days in each month (°C)
• temp5: mean January, February, March, and April temperature, weighted by the number of days in each month (°C)
• temp6: mean March and April temperature, weighted by the number of days in each month (°C)

File: sdat23.csv

Description: summarized shade phenology data on the plot level from 2023, excluding sham plots

Variables:

• date: date of observation
• site: site where observation was made, (G24 or ONA)
• plot: name of plot
• treatment: treatment of plot (ctrl, shade1, shade2, shade3, shade4, shade5, shade6)
• n_plants: total number of plants tagged in the plot
• obs_doy: Julian day of year observation was made
• shade_days: number of days of extra shade the plot received relative to the control plots
• sen_total: total number of plants that had senesced

File: sdat24.csv

Description: summarized shade phenology data on the plot level from 2024, excluding sham plots

Variables:

• date: date of observation
• site: site where observation was made, (G24 or ONA)
• plot: name of plot
• treatment: treatment of plot (ctrl, shade1, shade2, shade3, shade4, shade5, shade6)
• n_plants: total number of plants tagged in the plot
• obs_doy: Julian day of year observation was made
• shade_days: number of days of extra shade the plot received relative to the control plots
• sen_total: total number of plants that had senesced

File: sham.sdat23.csv

Description: summarized shade phenology data on the plot level from 2023, only sham and control plots

Variables:

• date: date of observation
• site: site where observation was made, (G24 or ONA)
• plot: name of plot
• treatment: treatment of plot (ctrl, sham1, sham2, sham3, sham4, sham5, sham6)
• n_plants: total number of plants tagged in the plot
• obs_doy: Julian day of year observation was made
• shade_days: number of days of extra shade the plot received relative to the control plots
• sen_total: total number of plants that had senesced

File: sham.sdat24.csv

Description: summarized shade phenology data on the plot level from 2024, only sham and control plots

Variables:

• date: date of observation
• site: site where observation was made, (G24 or ONA)
• plot: name of plot
• treatment: treatment of plot (ctrl, sham1, sham2, sham3, sham4, sham5, sham6)
• n_plants: total number of plants tagged in the plot
• obs_doy: Julian day of year observation was made
• shade_days: number of days of extra shade the plot received relative to the control plots
• sen_total: total number of plants that had senesced

File: sham.surv.flow.dat.csv

Description: survival, flowering, and fruiting data from control and sham plots in 2024

Variables:

• site: site where observation was made, (G24 or ONA)
• plot: name of plot
• id: individual plant ID
• flow24: indicator of flowering at all during the season (1 if flowering occurred, 0 if not)
• fru24: indicator of fruiting at all during the season (1 if fruiting occurred, 0 if not)
• alive24: indicator of year-to-year survival to 2024 (1 if survived, 0 if not)
• treatment: treatment of plot (ctrl, sham1, sham2, sham3, sham4, sham5, sham6)
• type: categorical indicator ctrl or sham
• n_plants: total number of plants tagged in the plot
• shade_days: number of days of extra shade the plot received relative to the control plots

File: soil.csv

Description: soil moisture measurement data collected with Campbell Scientific, HydroSense II Handheld Soil Moisture Sensor on a fair-weather day in March, 2023

Variables:

• moisture: soil moisture volumetric water content (VWC)
• treatment: treatment of plot at the time of measurement.

File: surv.flow.dat.csv

Description: survival, flowering, and fruiting data from control and shade plots in 2024

• site: site where observation was made, (G24 or ONA)
• plot: name of plot
• id: individual plant ID
• flow24: indicator of flowering at all during the season (1 if flowering occurred, 0 if not)
• fru24: indicator of fruiting at all during the season (1 if fruiting occurred, 0 if not)
• alive24: indicator of year-to-year survival to 2024 (1 if survived, 0 if not)
• treatment: treatment of plot (ctrl, shade1, shade2, shade3, shade4, shade5, shade6)
• n_plants: total number of plants tagged in the plot
• shade_days: number of days of extra shade the plot received relative to the control plots

File: 1_traipse_shade_phenology.R 

Description: This R script was used to analyze the phenology data (sdat23.csv, sdat24.csv, surv.flow.dat.csv, sham.sdat23.csv, sham.sdat24.csv, and sham.surv.flow.dat.csv). It reads the data, fits GLMs to understand how the shade treatment affected the phenology, and is used to create figure in Appendix S5, Figure 4, and Figure 5 in the manuscript. We used R version 4.4.2 (2024-10-31).

File: 2_traipse_shade_pendants.R

Description: This R script was used to analyze the pendant and soil moisture data (pendant.data.csv, and soil.csv). It reads the data, fits GLMs and runs Tukey's posthoc tests to compare environmental conditions between plots and treatments, and is used to create figures in Appendix S8 and Appendix S9. We used R version 4.4.2 (2024-10-31).

File: 3_traipse_shade_mismatch.R

Description: This R script was used to compare rate of phenological change between the spring ephemerals and the canopy. It reads the temperature data (prism_all.csv), tree phenology data (temp_evi.all.csv), peak flowering phenology data (temp_flowering.all_curves.csv), and MODIS data (modisveg_sub.csv) and compares rate of change of phenological event against temperature and time. Script used to create Figure 2, Figure 3, and figures in Appendix S6 and Appendix S7. We used R version 4.4.2 (2024-10-31).

File: MOD13Q1.061_script.docx, MOD13Q1.061_script.txt

Description: This Google Earth Engine script was used to download raw NDVI and EVI data from MOD13Q1.061 Terra Vegetation Indices 16-Day Global 250m. Code was run in Earth Engine Code Editor (code.earthengine.google.com) to extract data that can be found in modisveg_sub.csv file.