Dataset DOI: 10.5061/dryad.pc866t238

Description of the data and file structure

Summary of the dataset

This dataset originates from a split-plot factorial Open-Top Chamber (OTC) experiment at the Rhodes University Elevated CO₂ Facility (RUECF, South Africa). The study tested the interactive effects of ambient (400 ppm) and elevated (550 ppm) CO₂ concentrations and contrasting soil water availability on five southern African C₃ tree species:

1. Vachellia karroo
2. V. tortilis
3. V. sieberiana
4. V. robusta
5. Senegalia burkei

Seedlings were grown in OTCs from 2021–2023 and exposed to continuous CO₂ treatments and water manipulations. We measured gas exchange (ACi curves), soil water content, and growth. From the ACi curves, photosynthetic parameters (Vcmax, Jmax) were derived.

These datasets underpin all analyses, figures, and tables used in our Functional Ecology manuscript.

Files and variables

File: Parameter_data.csv

Description: Processed physiological and growth trait dataset derived from ACi curve fitting and harvest measurements. This file contains one row per individual plant (or measurement event) across CO₂ × water treatments and chambers. It is used for treatment-level trait comparisons in the manuscript (photosynthesis, stomatal conductance, Vcmax, Jmax, soil water status, and growth).

Variables

• Species: Vachellia karroo, V. tortilis, V. sieberiana, V. robusta, Senegalia burkei
• CO2.treatment: Growth CO₂ concentration: 400 ppm (ambient), 550 ppm (elevated)
• Chambers: Open top chamber ID (from 1 to 16)
• number: Plant/ individual identifier
• Cond: Stomatal conductance (g_ST, mol m^{-2 s}-1)
• Date: Measurement date
• Type: Measurement type (E- encroacher, NE- Nonencroacher)
• VWC: Volumetric water content at measurement 
• VWC_percent: Soil water content percentage
• SWC range: Soil water content bin/ range labels
• Ci: Intercellular CO₂ concentration
• Photo: Net photosynthesis at growth CO₂ (µmol m^{-2 s}-1)
• Vcmax: Maximum Rubisco carboxylation rate (µmol m^{-2 s}-1)
• Jmax: Maximum electron transport rate (µmol m^{-2 s}-1)
• TotalAGB: Above-ground dry biomass at harvest (g)
• Dates transplanted: Date seedlings transplanted into OTC pots
• Dates harvested: Date of destructive harvest

File: ACi.data.csv

Description: Processed ACi curve dataset containing treatment-level mean responses and model outputs for each species, water treatment, and CO₂ concentration. This file links observed photosynthetic rates with fitted carboxylation- and electron transport–limited assimilation values. It is used in the manuscript to plot A–Ci response curves.

Variables

• Water: water treatment (well-watered, droughted)

• Species: Species name (Vachellia karroo, V. tortilis, V. sieberiana, V. robusta, Senegalia burkei)

• CO₂.treatment: Growth CO₂ concentration (ppm)

• Ci: Intercellular CO₂ at each ACi step

• mean_Ac: Mean carboxylation-limited assimilation

• mean_Aj: Mean electron -transport- limited assimilation

• mean_A_predict: Model predicted net assimilation at that Ci

• sd_A_predict: SD of predicted assimilation across replicates/ fit

• Ac: Carboxylation-limited by other processes

• Ap: Assimilation limited by other processes/ partition

• Sp: Spare/ aux parameter from fit

• Aobs_mean: observed mean net assimilation at that Ci

• Aobs_sd: SD of observed net assimilation 

  Missing values are indicated as blank cells. Species taxonomy follows Vachellia/Senegalia updates. Ac, Aj, Aobs, and predictions are at saturating light and standard leaf temperature per protocol. Ap/Sp in the paper are model auxiliary outputs; not used in figures.

File: RawACi_curve.csv

Description: Raw ACi curve data collected at the leaf level from seedlings grown under CO₂ × water treatments. Contains per-curve raw observations (not averaged).

Variables

• Spp: Species name (Vachellia karroo, V. tortilis, V. sieberiana, V. robusta, Senegalia burkei)

• H2O.treat: Water treatment (watered, droughted)

• CO2.concentration: Growth chamber CO₂ concentration (400 ppm, 550 ppm)

• CO2S: Reference CO₂ concentration setpoint during measurement

• Curve: Curve replicate identifier (indicates replicate number within species × treatment).

• Ci: Intercellular CO₂ concentration measured during the ACi curve

• Photo: Net photosynthesis at that Ci (µmol m^{-2 s}-1).

• Tleaf: Leaf temperature during measurement (°C).

• PARi: Incident photosynthetic photon flux density (µmol m^{-2 s}-1).

  Measurements were made at saturating light (see PARi values) and steady-state conditions per curve. This raw file links directly to the processed dataset (ACi.data.csv) from which Vcmax, Jmax, and predicted values were derived

File: EJS_code.R

Description: Reproducible analysis and figure generation for the manuscript.
Scope:

• Code 1: Data import/cleaning, summary statistics, and multi-panel figures for A, g_ST, Ci, Vcmax, Jmax, and GrowthRate across CO₂ × soil water content × species.
• Code 2: Linear mixed-effects models for treatment and species contrasts; estimated marginal means and compact letter displays.
• Code 3: A–Ci response plotting workflow (per species and combined panels), directory setup, file name resolution, and session info export.

Software requirements:

• R ≥ 4.3 (tested on 4.3.x/4.4.x)
• R packages: ggplot2, ggpubr, gridExtra, dplyr,  ggmisc, ggtext, lme4, lmerTest, car, emmeans, lsmeans, readr, scales.

Working directory and project structure:
Run from the project root. The script will create the directories ./Data, ./Results, and ./Results/figures if they are missing. Place input files in ./Data. Figures and logs are written to ./Results/..

Data and variable expectations:

• Species factor uses updated Vachellia/Senegalia taxonomy.
• ACi variables (Ac, Aj, predictions, Aobs) are measured at saturating light and standard leaf temperature, as per the protocol.
• Column names are expected to match those in the provided CSVs (such as species, CO2.treatment as "400" / "550", Water as "Watered"/"Droughted", SWC or VWC_percent, Photo, Cond, Ci, Vcmax, Jmax, Chambers).

Reproducibility notes:

• The script writes sessionInfo.txt for transparency of platform and package versions.
• Mixed-effects model summaries and EMM/CLD tables are printed to the console; adapt the script if you wish to save them as a CSV file.

Access information

Other publicly accessible locations of the data:

• NA

Data was derived from the following sources:

• NA