DOI: 10.5061/dryad.gqnk98t2f
title: Data from: N₂-fixation is linked to the ability to encroach in African savanna trees

description: 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.
description: 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 (<sub>398 ppm) or elevated (545 ppm) CO</sub>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 δ<sup>15</sup>N
 using isotope ratio mass spectrometry. Percent nitrogen derived from
 fixation (% Ndfa) was calculated using shoot δ<sup>15</sup>N
 and reference non-nodulating plants. Soil δ<sup>15</sup>N was
 measured from 2 g topsoil samples collected from 30 pots.
 N-dynamic traits in the dataset include nodule mass fraction
 (NMF), leaf δ<sup>15</sup>N, stem δ<sup>15</sup>N,
 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)
description: # Data from: N₂-fixation is linked to the ability to encroach in African
 savanna trees Dataset DOI:
 [10.5061/dryad.gqnk98t2f](https://doi.org/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) 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