DOI: 10.5061/dryad.pc866t238
title: Savanna tree species show contrasting acclimation responses to elevated atmospheric CO<sub>2</sub> concentration and drought

description: How do savanna tree species adjust their photosynthetic performance when
 exposed to rising atmospheric CO2 and varying water availability? Do
 species differ in their capacity to upregulate photosynthesis under
 elevated CO2, and how are these responses constrained by drought? To
 address these questions, this dataset provides both raw and processed
 measurements on gas exchange and growth from an open-top chamber
 experiment that tested the interactive effects of CO2 (ambient: 400 ppm;
 elevated: 550 ppm) and soil water availability on five southern African C3
 tree species. The ACi curve dataset contains raw gas exchange
 measurements, including observed and modelled assimilation rates,
 carboxylation- and electron transport-limited photosynthesis, and
 intercellular CO2 concentration across treatments. The parameter dataset
 contains derived photosynthetic parameters (Vcmax, Jmax), leaf gas
 exchange traits (A, gST, Ci), soil water content (VWC), and plant
 performance variables (above-ground biomass), and chamber identifiers.
 These data directly support all analyses, figures, and tables in the
 manuscript, enabling reproduction of photosynthetic response curves,
 treatment comparisons, and species-level trait responses.
description: # Savanna tree species show contrasting acclimation responses to elevated
 atmospheric CO~2~ concentration and drought Dataset DOI:
 [10.5061/dryad.pc866t238](https://doi.org/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 CO~2~ Facility (RUECF, South
 Africa). The study tested the interactive effects of ambient (400 ppm) and
 elevated (550 ppm) CO~2~ concentrations and contrasting soil water
 availability on five southern African C~3~ 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 CO~2~ treatments and water manipulations. We measured gas
 exchange (ACi curves), soil water content, and growth. From the ACi
 curves, photosynthetic parameters (V*cmax*, J*max*) 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 CO~2~ × water
 treatments and chambers. It is used for treatment-level trait comparisons
 in the manuscript (photosynthesis, stomatal conductance, V*cmax*, J*max*,
 soil water status, and growth). ##### Variables * Species: *Vachellia
 karroo*, *V. tortilis*, *V. sieberiana*, *V. robusta*, *Senegalia burkei*
 * CO2.treatment: Growth CO~2~ 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 CO~2~ concentration * Photo: Net
 photosynthesis at growth CO~2~ (µmol m^-2 s^-1) * V*cmax*: Maximum Rubisco
 carboxylation rate (µmol m^-2 s^-1) * J*max*: 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
 CO~2~ 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)* * CO~2~.treatment: Growth CO~2~ concentration (ppm) * Ci:
 Intercellular CO~2~ 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 CO~2~ × 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 CO~2~
 concentration (400 ppm, 550 ppm) * CO2S: Reference CO~2~ concentration
 setpoint during measurement * Curve: Curve replicate identifier (indicates
 replicate number within species × treatment). * Ci: Intercellular CO~2~
 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 V*cmax*, J*max*, 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 CO~2~ × 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 ####