Data from: N₂-fixation is linked to the ability to encroach in African savanna trees

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. 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) CO}2~. 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) # Data from: N₂-fixation is linked to the ability to encroach in African savanna trees Dataset DOI: [10.5061/dryad.gqnk98t2f](doi.org) ## 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) CO~2~, and well-watered or water-limited soil conditions. Recorded traits include nodule mass fraction (NMF), leaf δ^15^N, stem δ^15^N, and percent nitrogen derived from fixation (% Ndfa). The dataset also includes metadata on species identity, encroacher status, CO~2~ and soil moisture treatments, replicate identifiers, and phylogenetic information. Soil δ^15^N 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 CO~2~ 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 — CO~2~ 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 δ^15^N relative to atmospheric N — Units: ‰ * Stem Total N % — Total nitrogen content in stem — Units: % * Stem Delta 15N vs Air — Stem δ^15^N 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 `readxl` package) — free and open source * **Python** (with `pandas` and `openpyxl`) — 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