Data and code from: Trade-offs and bet-hedging in clonal offspring allocation
Data files
May 27, 2026 version files 67.40 KB
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Oxalis_clonal_allocation_data_and_analysis_-_JoE.zip
60.67 KB
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README.md
6.73 KB
Abstract
This dataset contains the trait data, phylogenetic tree, and R code used to reproduce the analyses and figures in the study Trade-offs and bet-hedging in clonal offspring allocation in Oxalis (manuscript submitted to Ecology Letters). The raw trait data are then aggregated at the species level and matched to the phylogeny. The resulting dataset summarizes species-level means of belowground reproductive features, mainly bulbs, for Southern African species of Oxalis. Variables include total and mean offspring bulb mass and number, parental bulb size, and proportional allocation of offspring across five placement locations (disperser, spreader, upper, consolidator, lower). Additional variables describe the mass of belowground stems and contractile roots.
The R scripts for the analyses perform correlation analyses in their standard and phylogenetically informed versions, PCA and phylogenetic PCA of allocation patterns, clustering based on PCA components, and generation of publication figures.
All data and code are released under a CC0 public domain dedication. No sensitive information is included. The dataset enables full reproducibility of the results and figures contained in the submitted article.
This deposit contains the necessary data and R code required to reproduce the analyses and figures for the manuscript:
F. Curtis Lubbe, Lars Götzenberger, Roswitha Schmickl, Kenneth Oberlander, Tomáš Prochazká, and Jitka Klimešová (2026) Trade-offs and bet-hedging in clonal offspring allocation Journal of Ecology
Contents
Note that all data files and R code that are included and described below are not stored in this depository as single files, but are contained in a zipped folder, Oxalis_clonal_allocation_data_and_analysis_-_JoE.zip
.
├── data/
│ ├── data_oxalis.txt # Tidy species-level dataset used for analyses
│ └── tree_oxalis.txt # Species phylogeny in Newick format
├── code/
│ ├── figures_analyses.R # Main analysis & figure script
│ ├── apply_phy_cor.R # Helper: standard + phylogenetic correlations
│ └── optimize_clusters.R # Helper: realign cluster labels across runs
├── figures/ # Created by the script (see Section 4)
├── README.md # This file
└── sessionInfo.log # Info about the R version, loaded packages, etc.
Software requirements
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R ≥ 4.2 (tested under 4.4.x)
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R packages:
ape,tidyverse,FactoMineR,factoextra,phytools,clue,patchwork,svglite,fossilIf necessary, install with:
r install.packages(c("ape","tidyverse","FactoMineR","factoextra","phytools", "clue","patchwork","svglite","fossil"))
For full reproducibility, check the file "sessionInfo.log" that was created with the sessionInfo() function at completion of running the code in figures_analyses.R.
Data files
data/data_oxalis.txt
Rows are species; columns are variables. See the Placement locations for the meaning of the * placeholders in the variable names.
| Column | Description | Unit / scale |
|---|---|---|
g_average_bulb |
Mean offspring bulb mass per species | g |
N_total_bulbs |
Total number of offspring bulbs per species | count |
init_bw_g |
Initial parental bulb mass (before the growing season) | g |
g_average_bulb_log, N_total_bulbs_log |
log-transformed versions used in regressions | log |
g_*_clr, N_*_clr |
Centered log-ratio (clr) transformed allocations among placement locations (see below) | clr units |
g_*_perc, N_*_perc |
Percentage allocation among placement locations | % |
stem_total_g_clr, tunic_total_g_clr, contract_g_clr |
clr-transformed belowground structure masses (spacers, tunics, contractile roots) | clr units |
g_total_bulbs_clr |
clr-transformed total bulb mass | clr units |
biggest_bulb_g |
Mean mass of the biggest bulb per species | g |
depth_biggest_bulb_mm |
Mean depth of the biggest bulb per species | mm |
Placement locations (suffix legend):
disperser— bulbs placed at/above soil surfacespreader— bulbs placed horizontally away from the parentupper— bulbs placed above the parental bulb positionconsolidator— bulbs at the parental bulb position (within old tunics)lower— bulbs placed below the parental position- Missing values:
NA
data/tree_oxalis.txt
- Newick tree with tip labels matching species in
data_oxalis.txt(underscores converted to spaces in the script). Branch lengths present.
How to reproduce the results & figures
- Open
code/figures_analyses.Rin R (or RStudio). - Set the working directory to the repository root. The script uses relative paths:
data/,figures/,code/. - Running the script will:
- compute standard and phylogenetic correlations for the size–number trade-off,
- create phylogenetic residuals (Revell 2009) and compute standard and phylogenetic correlations for the size–number trade-off, but corrected for the parental bulb size,
- run PCA and phylogenetic PCA (PPCA) on allocation patterns,
- identify clusters (HCPC) and align cluster labels,
- generate the figures and save them to
figures/as SVG, with figure names and sequence according to the figures in the manuscript.
Expected outputs written to figures/:
figure1.svg— Offspring bulb mass vs number (on log–log scale).figure2b.svg— Belowground allocation PCA (axes labelled with variance explained).figure3bcde.svg— PCA biplots with barplots for offspring bulb weight and number.figureS1.svg— Mass of the biggest bulb vs depth of that bulb (on log–log scale).figureS2.svg— PCA biplots as the one shown in figure3bcde.svg, but the two biplots for bulb mass and bulb numbers are accompanied with their respective phylogenetic version for comparison.
If you prefer PDF/PNG, edit the svglite() calls in the script. Note that all figures have been modified slightly in a vector graphics software (Inkscape) for the final figures that are part of the manuscript.
License
All data and code in this archive are released under a CC0 1.0 Universal license (public domain dedication). Users are free to reuse, modify, and distribute without restriction.
Please cite the original article and this dataset DOI when reusing any part.
How to cite
- F. Curtis Lubbe, Lars Götzenberger, Roswitha Schmickl, Kenneth Oberlander, Tomáš Prochazká, and Jitka Klimešová(2026). Trade-offs and bet-hedging in clonal offspring allocation. Journal of Ecology.
- Lars Götzenberger and F. Curtis Lubbe (2026). Data and R code for: "Trade-offs and bet-hedging in clonal offspring allocation". Dryad. DOI: 10.5061/dryad.s7h44j1ms