Data from: N₂-fixation is linked to the ability to encroach in African savanna trees
Data files
Nov 26, 2025 version files 57.80 KB
-
Dated.tree
13.57 KB
-
nodule_biomass_15N.xlsx
38.46 KB
-
README.md
5.78 KB
Abstract
This dataset includes nitrogen (N) dynamics for 12 southern African savanna tree species (six encroachers, six non-encroachers) under manipulated atmospheric CO2 (~398 ppm ambient, ~545 ppm elevated) and soil moisture (well-watered vs water-limited) in open-topped chambers. Measured traits include nodule mass fraction, leaf and stem δ15N, and percentage of N derived from N2-fixation (% Ndfa). The data capture both short- and long-term N allocation strategies and enable exploration of how CO2 and water treatments affect N dynamics across encroaching and non-encroaching species.
Dataset DOI: 10.5061/dryad.gqnk98t2f
Description of the data and file structure
The dataset contains measurements of nitrogen (N) dynamics for 12 southern African savanna tree species (six encroachers, six non-encroachers) grown under ambient (~398 ppm) and elevated (545 ppm) CO2, and well-watered or water-limited soil conditions. Recorded traits include nodule mass fraction (NMF), leaf δ15N, stem δ15N, and percent nitrogen derived from fixation (% Ndfa). The dataset also includes metadata on species identity, encroacher status, CO2 and soil moisture treatments, replicate identifiers, and phylogenetic information. Soil δ15N measurements are provided for reference. These data allow comparison of short- and long-term N allocation strategies across species and treatments and can be used to explore the role of N2-fixation in plant responses to elevated CO2 and variable water availability.
Files and variables
File: nodule_biomass_15N.xlsx
Description: N-dynamic trait data
Variables
- ID number — Unique plant identifier — Units: —
- OTC — Open-top chamber number — Units: Categorical (1-16)
- Species — Species name — Units: Categorical (Vachellia_sieberiana_var_woodii; Vachellia_robusta_subsp_clavigera; Vachellia_karroo; Vachellia_nilotica; Vachellia_swazica; Vachellia_grandicornuta; Vachellia_exuvialis; Vachellia_tortilis; Vachellia_erioloba)
- Encroacher status — Current encroacher classification — Units: Categorical (Encroacher; Non-encroacher)
- CO2 treatment — CO2 treatment applied — Units: Categorical (ambient; elevated)
- Soil moisture treatment — Soil moisture treatment applied — Units: Categorical (well-watered; water-limited)
- Leaf Total N % — Total nitrogen content in leaves — Units: %
- Leaf Delta 15N vs Air — Leaf δ15N relative to atmospheric N — Units: ‰
- Stem Total N % — Total nitrogen content in stem — Units: %
- Stem Delta 15N vs Air — Stem δ15N relative to atmospheric N — Units: ‰
- Stem Total C % — Total carbon content in stem — Units: %
- Total coarse root mass (g) — Mass of coarse roots — Units: g
- Total fine root mass (g) — Mass of fine roots — Units: g
- Total belowground biomass (g) — Total root biomass (coarse + fine) — Units: g
- Total nodule mass (g) — Mass of N2-fixing nodules — Units: g
- Total belowground mass (g) — Total belowground biomass including nodules — Units: g
- Nodule mass fraction (%) — Fraction of total belowground biomass made up of nodules — Units: %
- Total coarse root mass (g) — Mass of coarse roots — Units: g
- Total fine root mass (g) — Mass of fine roots — Units: g
- Total belowground biomass (g) — Total root biomass (coarse + fine) — Units: g
- Total nodule mass (g) — Mass of N2-fixing nodules — Units: g
- Total belowground mass (g) — Total belowground biomass including nodules — Units: g
- Nodule mass fraction (%) — Fraction of total belowground biomass made up of nodules — Units: %
File: Dated.tree
Description: Phlogenetic Tree data
Variables
- ID number — Unique node/branch identifier — Units: —
- Taxon — Taxon name — Units: Categorical (Desmanthus_bicornutus; Senegalia_burkei; Senegalia_caffra; Senegalia_nigrescens; Vachellia_erioloba; Vachellia_exuvialis; Vachellia_grandicornuta; Vachellia_karroo; Vachellia_nilotica; Vachellia_robusta_subsp_clavigera; Vachellia_sieberiana_var_woodii; Vachellia_swazica; Vachellia_tortilis)
- Height — Node height — Units: substitutions per site (or millions of years if scaled)
- Height 95% HPD — 95% highest posterior density interval for node height — Units: substitutions per site
- Height median — Median node height — Units: substitutions per site
- Height range — Range of sampled node heights — Units: substitutions per site
- Branch length — Branch length — Units: substitutions per site
- Branch length 95% HPD — 95% highest posterior density interval for branch length — Units: substitutions per site
- Branch length median — Median branch length — Units: substitutions per site
- Branch length range — Range of sampled branch lengths — Units: substitutions per site
- Rate — Substitution rate along branch — Units: substitutions per site per unit time
- Rate 95% HPD — 95% highest posterior density interval for substitution rate — Units: substitutions per site per unit time
- Rate median — Median substitution rate — Units: substitutions per site per unit time
- Rate range — Range of sampled substitution rates — Units: substitutions per site per unit time
- Posterior probability — Posterior probability of node support — Units: —
Code/software
The dataset includes Excel (.xlsx) files and a phylogenetic tree (.tree) file. All files are provided in open or widely supported formats, and no proprietary software is required.
Excel files (.xlsx)
These can be opened using any of the following free or open-source programs:
- LibreOffice Calc (free, open source)
- Google Sheets (free, web-based)
- R (with the
readxlpackage) — free and open source - Python (with
pandasandopenpyxl) — free and open source
They are also compatible with Microsoft Excel, though not required.
Phylogenetic tree file (.tree)
The .tree file is in standard Newick format and can be opened or analysed with:
- R (packages:
ape,phytools) - FigTree (free tree viewer)
- iTOL (Interactive Tree of Life; free for non-commercial use)
- Any Newick-compatible tree viewer or text editor
The dataset comprises 12 southern African savanna tree species (nine Vachellia, three Senegalia), with six encroachers and six non-encroachers. All species are facultative N2-fixers. Seeds were obtained from SilverHill Seeds (Cape Town, South Africa), heat-treated at 80 °C for 10 minutes to break dormancy, germinated in November 2021, and transplanted into individual cylindrical pots (20 cm diameter × 75 cm height) containing sieved savanna soil from Fort Beaufort, Eastern Cape, South Africa.
Plants were grown in 16 open-top chambers at Rhodes University Elevated CO2 Facility (Makhanda, South Africa) under ambient (398 ppm) or elevated (545 ppm) CO2~. Soil moisture treatments included well-watered (daily irrigation to ~0.30 volumetric soil moisture) and water-limited (ambient rainfall, ~0.24 SMC). Treatments were fully crossed with approximately five replicates per species per treatment.
Plants were destructively harvested at 11 months. Above- and belowground biomass were separated, oven-dried, and weighed. Nodules were collected, dried, and weighed. Leaf and stem tissues were milled and analyzed for δ15N using isotope ratio mass spectrometry. Percent nitrogen derived from fixation (% Ndfa) was calculated using shoot δ15N and reference non-nodulating plants. Soil δ15N was measured from 2 g topsoil samples collected from 30 pots.
N-dynamic traits in the dataset include nodule mass fraction (NMF), leaf δ15N, stem δ15N, and % Ndfa. Phylogenetic relationships among species were incorporated using a time-calibrated tree based on plastid markers (trnL-F, matK, trnH-psbA). Phylogenetic signal (Pagel’s λ) and bivariate trait relationships are provided to account for shared evolutionary history (file = dated.tree)