Comparative evolution of photosynthetic light response curves: Approaches and pitfalls in phylogenetic modeling of a function-valued trait
Data files
Mar 04, 2026 version files 135.65 KB
-
Davis_etal_2026_Dataset.csv
112.81 KB
-
Davis_etal_2026_Metadata.csv
2.82 KB
-
README.md
20.03 KB
Abstract
Plant adaptation to diverse conditions includes species divergence in photosynthetic physiology. This dataset contains photosynthetic light response curve data collected on a single germplasm accession for each of 28 diverse wild sunflower species (genus Helianthus) grown under controlled greenhouse conditions. Gas exchange data was collected using a TARGAS-1 portable photosynthesis system, with standard outputs for this instrument provided at each data point collected across nine light levels from complete darkness to 2500 micromoles per meter squared per second of photosynthetically active radiation flux.
The dataset includes directly measured values (reference and analysis values for carbon dioxide and water vapor, atmospheric pressure and flow rate, exterior and interior light levels, and cuvette temperature), as well as calculated values (leaf temperature, transpiration rate, vapor pressure deficit, stomatal conductance, net photosynthetic assimilation, and intercellular carbon dioxide concentration). Note that four species with narrow leaves did not fill the chamber cuvette (see article for adjustment method), and 3% of data points have partially missing data values due to the instrument entering auto-zero cycle.
The dataset was used to conduct function-valued trait (FVT) modeling of the evolution of light curves with phylogenetic comparative methods. The dataset could be used as part of meta-analysis or synthesis requiring light response curve data, with appropriate considerations of data limitations.
Dataset DOI: 10.5061/dryad.2v6wwq03f
Description of the data and file structure
This dataset contains photosynthetic light response curve data collected on a single germplasm accession for each of 28 diverse wild sunflower species (genus Helianthus) grown under controlled greenhouse conditions. Gas exchange data was collected using a TARGAS-1 portable photosynthesis system, with standard outputs for this instrument provided at each data point collected across nine light levels from complete darkness to 2500 micromoles per meter squared per second of photosynthetically active radiation flux.
Files and variables
File: Davis_etal_2026_Dataset.csv
Description: Dataset containing 666 rows of gas exchange data points collected within the experiment.
| Variable | Description |
| Species | Identity of the Helianthus species |
| Accession | USDA Plant Introduction (PI) number for the germplasm accession within the National Plant Germplasm System (seed derived from a wild population and deposited with NPGS). PI number can be queried in the USDA Germplasm Resources Information Network for more information on source locality, date of collection, and characteristics. |
| Replicate | Replicate plant number within the experiment. |
| Date | Date light curve was collected (YYYY-MM-DD) |
| Time | Time of day light curve was collected, in local time, 24-hour format (HH:MM:SS) |
| Rec.Number | Measurement recording number (arbitrary) |
| CO2r | Reference CO2 concentration (ppm) - air entering cuvette |
| CO2a | Analysis CO2 concentration (ppm) - air exiting cuvette |
| H2Or | Reference H2O reading (millibars) - air entering cuvette |
| H2Oa | Analysis H2O reading (millibars) - air exiting cuvette |
| atm | atmospheric pressure (millibars) |
| Flow.Supply | Supply flow (cubic centimeters per minute) |
| Flow.sample | Sample flow (cubic centimeters per minute) |
| Ext.type | Extension type. 14=normal operation, 71=instument in auto-zero cycle. Note that as measurements were manually recorded (initiated by button press upon verifying stability of gas exchange), data collected just as the instrument entered an auto-rezero cycle provides the last valid measurement of photosynthetic assimilation rate (A) but lacks various other output data. All output variables were observed to be stable and within reasonable ranges at the time of recording, but were not captured in the data record if the instrument entered auto-zero cycle (Ext.type =71) in the few seconds between verification and pressing "record". This affects approcimately 3% of data records. NA values represent variables not recorded by the instrument. |
| PARe | External ambient photosynthetically active radiation (PAR) flux in micromoles per meter squared per second |
| PARi | Internal photosynthetically active radiation (PAR) flux (micromoles per meter squared per second), inside the cuvette as controlled by the LED light unit. |
| Tcuv | Temperature inside the cuvette (Celsius) |
| Tleaf | Temperature of the leaf (Celsius) |
| Trans | Transpiration rate (millimoles H2O per square meter per second) |
| VPD | Vapor pressure deficit (millibars) |
| gs | Stomatal conductance (millimoles H2O per square meter per second) |
| A | Net photosynthetic assimilation (micromoles CO2 per square meter per second) |
| Ci | Intercellular CO2 concentration (ppm) |
| Area | Leaf area within the cuvette (square centimeters). A filled cuvette is 4.5 square centimeters of leaf. Unfilled cuvettes are denoted. Gas exchange for an unfilled cuvette was adjusted by estimated leaf area as described in text and code. |
| RepDate | Concatenation of Replicate and Date. |
| SpeciesRepDate | Concatenation of Species with RepDate. |
File: Davis_etal_2026_Metadata.csv
Description: Contains identical metadata information as listed above, with variable names and descriptions.
Code/software
CSV files (dataset, metadata) can be opened with any software capable of reading comma separated value formats.
The included file directory contains the RMarkdown file and related R code and input files used for analysis. R Statistical Software version 4.2.3 was used for analysis and creation of R project files and RMarkdown.
Access information
Not applicable.
