Dataset DOI: 10.5061/dryad.2rbnzs83c

Description of the data and file structure

Files and variables

File: Chadwick_ProcB_10.1098_rspb.2025.1721_DatasetS1.csv

Description: Metadata file that provides nomenclature and trait data for every species-by-plot (i.e. a species that occurs in n plots is represented n times), including mean metabolome chemical properties, morphological trait values, and abudance-weighted chemical similarity to co-occurring species with respect to metabolites that represent the upper or lower quartile of metabolites for particular chemical properties. NA indicates data not available in the Madidi Project morphological traits dataset.

Variables

• sampleCode: Name of the LC-MS data file
• speciesCode: Six-character species code or morpho-species code
• Plot: Madidi Project forest plot
• Species_binomial: Species Latin binomial
• Genus: Botanical genus
• Family: Botanical family
• Abundance: Number of individuals in the forest plot
• nAtomP: The number of atoms in the largest aromatic, conjugated pi system, which is high in pigments and light-absorbing molecules that function to protect plants from ultraviolet radiation.
• ALogP: Hydrophobicity measured as the log-ratio of solubility in octanol versus water; may be related to a plant-defense spectrum defined by unsaturated, aromatic, and nonpolar metabolites versus saturated and polar metabolites; negatively correlated with polarity and hence desiccation resistance.
• TopoPSA: Topological polar surface area, the sum of the surface area of polar atoms in Ångstroms (Å), which may contribute to desiccation resistance, but is negatively correlated with passive transport through cell membranes.
• Fsp3: The fraction of carbon atoms with sp3 electron orbits (i.e. only single bonds) to the total number of carbon atoms in the molecule, which is positively correlated with melting point, solubility, and the likelihood of a compound to exhibit bioactivity in pharmaceutical assays.
• MW: Molecular weight in Daltons (Da); greatest in peptides and lignans, may be related to leaf longevity because peptides and lignans function as long-lived physical and storage structures.
• SLA: Specific leaf area; a leaf economics-resource capture trait associated with high photosynthetic rates, high relative growth rates, low carbon investment in lignin or tannins, and resource-rich environments. NA indicates data not available in the Madidi Project morphological traits dataset.
• LeafArea: Leaf area; associated with a resource-acquisitive life history strategy. NA indicates data not available in the Madidi Project morphological traits dataset.
• LeafThickness: Leaf thickness; associated with tolerance to disturbance and nutrient stress and a resource-conservative life history strategy. NA indicates data not available in the Madidi Project morphological traits dataset.
• TwigBarkThickness_Relative: Twig bark thickness relative to stem diameter; associated with protection from attack by pathogens and herbivores. NA indicates data not available in the Madidi Project morphological traits dataset.
• TwigSpecDens: Twig specific density; associated with low relative growth rates, high survival, and resistance to pathogens, herbivores or physical damage. NA indicates data not available in the Madidi Project morphological traits dataset.
• nAtomP_75: Abundance-weighted CSCS chemical similarity to co-occurring tree species with respect to the upper quartile of metabolites with respect to nAtomP
• ALogP_25: Abundance-weighted CSCS chemical similarity to co-occurring tree species with respect to the lower quartile of metabolites with respect to ALogP
• TopoPSA_75: Abundance-weighted CSCS chemical similarity to co-occurring tree species with respect to the upper quartile of metabolites with respect to TopoPSA
• TopoPSA_25: Abundance-weighted CSCS chemical similarity to co-occurring tree species with respect to the lower quartile of metabolites with respect to TopoPSA
• Fsp3_75: Abundance-weighted CSCS chemical similarity to co-occurring tree species with respect to the upper quartile of metabolites with respect to Fsp3
• Elevation: Elevation of the forest plot in which the species occurs in meters (m)
• Plot_simp: Simplified name of the forest plot

File: Chadwick_ProcB_10.1098_rspb.2025.1721_DatasetS2.csv

Description: Data table of variables defined for each of the 16 Madidi forest plots used in the study, including elevation, climate, phylogenetic similarity, abundance-weighted mean chemical properties, and abundance-weighted mean chemical similarity of co-occurring species with respect to suites of compounds that represent upper or lower quartiles of metabolites with respect to particular chemical properties.

Variables

• Plot: Madidi Project forest plot
• Elevation: Elevation of the forest plot in meters (m).
• Climate_PC1: Position of the forest plot on the first principal component in a principal component analysis (PCA); greater values reflect greater temperature and precipitation.
• Climate_PC2: Position of the forest plot on the second principal component in a principal component analysis (PCA); greater values reflect precipitation and temperature seasonality.
• invSimpson: Species diversity represented as the inverse Simpson index.
• nAtomP: Community-weighted mean nAtomP, the number of atoms in the largest aromatic, conjugated pi system, which is high in pigments and light-absorbing molecules that function to protect plants from ultraviolet radiation.
• ALogP: Community-weighted mean ALogP, hydrophobicity measured as the log-ratio of solubility in octanol versus water; may be related to a plant-defense spectrum defined by unsaturated, aromatic, and nonpolar metabolites versus saturated and polar metabolites; negatively correlated with polarity and hence desiccation resistance.
• TopoPSA: Community-weighted mean TopoPSA, topological polar surface area, the sum of the surface area of polar atoms in Ångstroms (Å), which may contribute to desiccation resistance, but is negatively correlated with passive transport through cell membranes.
• Fsp3: Community-weighted mean Fsp3, the fraction of carbon atoms with sp3 electron orbits (i.e. only single bonds) to the total number of carbon atoms in the molecule, which is positively correlated with melting point, solubility, and the likelihood of a compound to exhibit bioactivity in pharmaceutical assays.
• MW: Community-weighted mean molecular weight in Daltons (Da); greatest in peptides and lignans, may be related to leaf longevity because peptides and lignans function as long-lived physical and storage structures.
• SLA: Community-weighted mean specific leaf area; a leaf economics-resource capture trait associated with high photosynthetic rates, high relative growth rates, low carbon investment in lignin or tannins, and resource-rich environments.
• LeafArea: Community-weighted mean leaf area; associated with a resource-acquisitive life history strategy.
• LeafThickness: Community-weighted mean leaf thickness; associated with tolerance to disturbance and nutrient stress and a resource-conservative life history strategy.
• TwigBarkThickness_Relative: Community-weighted mean twig bark thickness relative to stem diameter; associated with protection from attack by pathogens and herbivores.
• TwigSpecDens: Community-weighted mean twig specific density; associated with low relative growth rates, high survival, and resistance to pathogens, herbivores or physical damage.
• PhyloPCoA1: Position of the forest plot on the first axis of a principal coordinates analysis that reflects the phylogenetic similarity among the 16 forest plots
• PhyloPCoA2: Position of the forest plot on the second axis of a principal coordinates analysis that reflects the phylogenetic similarity among the 16 forest plots
• nAtomP_75: Community (abundance)-weighted mean CSCS chemical similarity of species to other co-occurring tree species with respect to metabolites in the upper quartile of nAtomP
• ALogP_25: Community (abundance)-weighted mean CSCS chemical similarity of species to other co-occurring tree species with respect to metabolites in the lower quartile of ALogP
• TopoPSA_75: Community (abundance)-weighted mean CSCS chemical similarity of species to other co-occurring tree species with respect to metabolites in the upper quartile of TopoPSA
• TopoPSA_25: Community (abundance)-weighted mean CSCS chemical similarity of species to other co-occurring tree species with respect to metabolites in the lower quartile of TopoPSA
• Fsp3_75: Community (abundance)-weighted mean CSCS chemical similarity of species to other co-occurring tree species with respect to metabolites in the upper quartile of Fsp3

File: Chadwick_ProcB_10.1098_rspb.2025.1721_DatasetS3.tre

Description: Qemistree dendrogram that reflects the structural similarity among metabolites. Tip labels correspond to LC-MS feature IDs in Dataset S4.

File: Chadwick_ProcB_10.1098_rspb.2025.1721_DatasetS4.csv

Description: Metabolome mastertable that contains metabolite annotations, including predicted structures, classifications, chemical properties, and abundance in each sample. NAs indicate missing annotations due to insufficient data.

Variables

• id: Metabolite feature ID number generated by Qemistree; matches tip labels in the Qemistree dendrogram.
• X.featureID: Metabolite feature ID number generated by MZmine.
• csi_smiles: Predicted structure generated by Sirius.
• table_number: Dataset input number for Qemistree
• smiles: Predicted structure generated by Sirius.
• structure_source: Sirius module used to predict metabolite chemical structure.
• kingdom: Classyfire chemotaxonomical classification at the kingdom level.
• superclass: Classyfire chemotaxonomical classification at the superclass level.
• class: Classyfire chemotaxonomical classification at the class level.
• subclass: Classyfire chemotaxonomical classification at the subclass level.
• direct_parent: Classyfire chemotaxonomical classification at the most-specific, direct-parent level.
• class_results: NPClassifier chemotaxonomical classification at the class level.
• superclass_results: NPClassifier chemotaxonomical classification at the superclass level.
• pathway_results: NPClassifier chemotaxonomical classification at the biosynthetic pathway level.
• isglycoside: NPClassifier indicator, whether the metabolite is a glycoside (contains a sugar moiety).
• custom: Classification used by the authors.
• MW: Molecular weight in Daltons (Da); greatest in peptides and lignans, may be related to leaf longevity because peptides and lignans function as long-lived physical and storage structures.
• nAtom: Number of atoms.
• naAromAtom: Number of aromatic atoms
• nAtomLC: Number of atoms in the longest chain.
• nAtomP: The number of atoms in the largest aromatic, conjugated pi system, which is high in pigments and light-absorbing molecules that function to protect plants from ultraviolet radiation.
• nB: Number of bonds
• nAromBond: Number of aromatic bonds
• nRotB: Number of rotatable bonds.
• XLogP: Octanol/water partition coefficient calculated using a modified atom-additive model summing atomic contributions and correcting for intramolecular interactions; positive indicates affinity to octanol (i.e. nonpolar, hydrophobic), negative to water (i.e. polar, hydrophilic);
• ALogP: Octanol/water partition coefficient calculated using a modified atom-additive model summing atom type contributions based on focal atom and bond characteristics; positive indicates affinity to octanol (i.e. nonpolar, hydrophobic), negative to water (i.e. polar, hydrophilic); may be related to a plant-defense spectrum defined by unsaturated, aromatic, and nonpolar metabolites versus saturated and polar metabolites; negatively correlated with polarity and hence desiccation resistance.
• MLogP: Octanol/water partition coefficient calculated using a simple equation dependent on the number of C atoms and number of hetero atoms; smaller indicates affinity to octanol (i.e. nonpolar, hydrophobic), larger to water (i.e. polar, hydrophilic);
• TopoPSA: Topological polar surface area, the sum of the surface area of polar atoms in Ångstroms (Å), which may contribute to desiccation resistance, but is negatively correlated with passive transport through cell membranes.
• tpsaEfficiency: Molecular weight-specific topological polar surface area, the sum of the surface area of polar atoms in Ångstroms divided by the molecular weight in Daltons (Å Da^-1), which may contribute to desiccation resistance, but is negatively correlated with passive transport through cell membranes.
• HybRatio: Fraction of sp3 to sp2 carbon atoms; proxy for bond saturation and three-dimensional topological complexity, which is positively correlated with melting point, solubility, and the likelihood of a compound to exhibit bioactivity in pharmaceutical assays.
• Fsp3: The fraction of carbon atoms with sp3 electron orbits (i.e. only single bonds) to the total number of carbon atoms in the molecule, which is positively correlated with melting point, solubility, and the likelihood of a compound to exhibit bioactivity in pharmaceutical assays.
• FMF: Ratio between size of molecular framework (ring atoms plus linkers) and size of metabolite; complexity measure positively correlated with promiscuity (number of protein targets >50% inhibited) at values above 0.65.
• ECCEN:  Eccentric connectivity index, the distance-cum-adjacency topological descriptor; higher for longer chains with less branching; correlated with size and physicochemical properties such as boiling point.
• WPATH: Wiener path number, a topological descriptor of molecular branching that can differentiate structural isomers; correlated positively with size and boiling point.
• WPOL: Wiener polarity number, a variant of the Wiener path number calculated using vertices (C atoms) at distance 3; correlated positively with size and boiling point.
• nHBDon: Number of hydrogen-bond donors (e.g. OH, NH, formal charge ≥ 0).
• nHBAcc: Number of hydrogen-bond acceptors (e.g. O/N, formal charge ≤ 0, non-ether O, non-adjacent ON)
• PC1: Position on the first principal component of a principal component analysis on metabolite chemical properties.
• PC2: Position on the second principal component of a principal component analysis on metabolite chemical properties.
• PC3: Position on the third principal component of a principal component analysis on metabolite chemical properties.
• PC4: Position on the fourth principal component of a principal component analysis on metabolite chemical properties.
• PC5: Position on the fifth principal component of a principal component analysis on metabolite chemical properties.
• MDP0209.mzXML.Peak.area: Area under the curve of the chromatographic peak representing the quantity of the metabolite in sample MDP0209.mzXML; all subsequent columns columns display quantification data for pools representing every unique tree species-by-forest plot combination (906 species-by-plot).
• MDP0213.mzXML.Peak.area:
• MDP0206.mzXML.Peak.area:
• MDP0221.mzXML.Peak.area:
• MDP0211.mzXML.Peak.area:
• MDP0215.mzXML.Peak.area:
• MDP0212.mzXML.Peak.area:
• MDP0204.mzXML.Peak.area:
• MDP0220.mzXML.Peak.area:
• MDP0208.mzXML.Peak.area:
• MDP0214.mzXML.Peak.area:
• MDP0223.mzXML.Peak.area:
• MDP0207.mzXML.Peak.area:
• MDP0224.mzXML.Peak.area:
• MDP0219.mzXML.Peak.area:
• MDP0222.mzXML.Peak.area:
• MDP0210.mzXML.Peak.area:
• MDP0205.mzXML.Peak.area:
• MDP0216.mzXML.Peak.area:
• MDP0203.mzXML.Peak.area:
• MDP0218.mzXML.Peak.area:
• MDP0217.mzXML.Peak.area:
• MDP0587.mzXML.Peak.area:
• MDP0585.mzXML.Peak.area:
• MDP0572.mzXML.Peak.area:
• MDP0586.mzXML.Peak.area:
• MDP0571.mzXML.Peak.area:
• MDP0554.mzXML.Peak.area:
• MDP0580.mzXML.Peak.area:
• MDP0596.mzXML.Peak.area:
• MDP0553.mzXML.Peak.area:
• MDP0561.mzXML.Peak.area:
• MDP0576.mzXML.Peak.area:
• MDP0582.mzXML.Peak.area:
• MDP0594.mzXML.Peak.area:
• MDP0545.mzXML.Peak.area:
• MDP0573.mzXML.Peak.area:
• MDP0574.mzXML.Peak.area:
• MDP0568.mzXML.Peak.area:
• MDP0579.mzXML.Peak.area:
• MDP0548.mzXML.Peak.area:
• MDP0583.mzXML.Peak.area:
• MDP0599.mzXML.Peak.area:
• MDP0534.mzXML.Peak.area:
• MDP0584.mzXML.Peak.area:
• MDP0563.mzXML.Peak.area:
• MDP0529.mzXML.Peak.area:
• MDP0528.mzXML.Peak.area:
• MDP0593.mzXML.Peak.area:
• MDP0567.mzXML.Peak.area:
• MDP0549.mzXML.Peak.area:
• MDP0543.mzXML.Peak.area:
• MDP0564.mzXML.Peak.area:
• MDP0535.mzXML.Peak.area:
• MDP0537.mzXML.Peak.area:
• MDP0551.mzXML.Peak.area:
• MDP0559.mzXML.Peak.area:
• MDP0532.mzXML.Peak.area:
• MDP0542.mzXML.Peak.area:
• MDP0546.mzXML.Peak.area:
• MDP0547.mzXML.Peak.area:
• MDP0569.mzXML.Peak.area:
• MDP0565.mzXML.Peak.area:
• MDP0541.mzXML.Peak.area:
• MDP0555.mzXML.Peak.area:
• MDP0556.mzXML.Peak.area:
• MDP0558.mzXML.Peak.area:
• MDP0544.mzXML.Peak.area:
• MDP0591.mzXML.Peak.area:
• MDP0539.mzXML.Peak.area:
• MDP0581.mzXML.Peak.area:

File: DisciplineSpecificMetadata.json

Description:

The DisciplineSpecificMetadata.json file contains parameter values for experimental and instrumental protocols used in liquid chromatography-mass spectrometry (LC-MS) data collection.

Code/software

File: Chadwick_ProcB_10.1098_rspb.2025.1721.R

R code used for Chadwick, Sierra E., David Henderson, Dale L. Forrister, Leslie Cayola, Alfredo F. Fuentes, Belén Alvestegui, Nathan Muchhala, J. Sebastián Tello, Martin Volf, Jonathan A. Myers, and Brian E. Sedio. Proceedings B (https://doi.org/10.1098/rspb.2025.1721) is provided in the file. This file includes R code used for data manipulation, statistical analyses, and data visualization/figure creation for the Chadwick et al. Proc B manuscript. R version 4.4.1 on Mac OS 15.5.

The R code assumes that the four supplementary data files are located in a folder with the path: ~Documents/Madidi_Project

R package versions used in the file:

# attached base packages:

# [1] stats     graphics  grDevices utils     datasets  methods   base     

# other attached packages:

 # [1] V.PhyloMaker2_0.1.0 plotly_4.10.4       adiv_2.2.1          phylosignal_1.3.1   picante_1.8.2      

 # [6] nlme_3.1-167        phytools_2.4-4      maps_3.4.2.1        ape_5.8-1           corrplot_0.95      

# [11] ggrepel_0.9.6       ggplot2_3.5.1       vegan_2.6-10        lattice_0.22-6      permute_0.9-7      

# loaded via a namespace (and not attached):

  # [1] DBI_1.2.3               mnormt_2.1.1            deldir_2.0-4            phangorn_2.12.1        

  # [5] rlang_1.1.5             magrittr_2.0.3          ade4_1.7-22             compiler_4.4.1         

  # [9] mgcv_1.9-1              png_0.1-8               vctrs_0.6.5             reshape2_1.4.4         

 # [13] combinat_0.0-8          quadprog_1.5-8          stringr_1.5.1           pkgconfig_2.0.3        

 # [17] crayon_1.5.3            fastmap_1.2.0           promises_1.3.2          rmarkdown_2.29         

 # [21] purrr_1.0.2             xfun_0.52               seqinr_4.2-36           clusterGeneration_1.3.8

 # [25] jsonlite_1.8.9          progress_1.2.3          later_1.4.1             adegenet_2.1.10        

 # [29] uuid_1.2-1              jpeg_0.1-10             parallel_4.4.1          prettyunits_1.2.0      

 # [33] cluster_2.1.8           R6_2.5.1                stringi_1.8.4           RColorBrewer_1.1-3     

 # [37] boot_1.3-31             numDeriv_2016.8-1.1     Rcpp_1.0.14             iterators_1.0.14       

 # [41] knitr_1.49              optimParallel_1.0-2     base64enc_0.1-3         adephylo_1.1-16        

 # [45] httpuv_1.6.15           Matrix_1.7-2            adegraphics_1.0-21      splines_4.4.1          

 # [49] igraph_2.1.4            tidyselect_1.2.1        yaml_2.3.10             phylobase_0.8.12       

 # [53] doParallel_1.0.17       codetools_0.2-20        tibble_3.2.1            plyr_1.8.9             

 # [57] shiny_1.10.0            withr_3.0.2             coda_0.19-4.1           evaluate_1.0.3         

 # [61] xml2_1.3.6              lpSolve_5.6.23          pillar_1.10.1           KernSmooth_2.23-26     

 # [65] foreach_1.5.2           generics_0.1.3          sp_2.2-0                hms_1.1.3              

 # [69] munsell_0.5.1           scales_1.3.0            xtable_1.8-4            rncl_0.8.7             

 # [73] glue_1.8.0              lazyeval_0.2.2          scatterplot3d_0.3-44    tools_4.4.1            

 # [77] interp_1.1-6            data.table_1.16.4       rgl_1.3.17              XML_3.99-0.18          

 # [81] fastmatch_1.1-6         grid_4.4.1              tidyr_1.3.1             RNeXML_2.4.11          

 # [85] crosstalk_1.2.1         latticeExtra_0.6-30     colorspace_2.1-1        cli_3.6.3              

 # [89] DEoptim_2.2-8           expm_1.0-0              viridisLite_0.4.2       dplyr_1.1.4            

 # [93] gtable_0.3.6            digest_0.6.37           farver_2.1.2            htmlwidgets_1.6.4      

 # [97] htmltools_0.5.8.1       lifecycle_1.0.4         httr_1.4.7              mime_0.12              

# [101] MASS_7.3-64  

Access information

Other publicly accessible locations of the data:

• The raw data from the Madidi Project are stored and managed in Tropicos (https://tropicos.org/home), the botanical database of the Missouri Botanical Garden. The data for each forest plot can be accessed via the Madidi Project Plot Search page (http://tropicos.org/PlotSearch.aspx?projectid=20).
• The raw LC-MS spectra were deposited as a public MassIVE dataset on the Global Natural Products Social (GNPS) Molecular Networking server (https://massive.ucsd.edu/ProteoSAFe/dataset_files.jsp?task=a4a891a0f3b3467fb790a9c335783205#%7B%22table_sort_history%22%3A%22main.collection_asc%22%7D) with FTP download link (ftp://massive.ucsd.edu/MSV000090549) and doi (https://doi.org/10.25345/C52R3P21H).