Dataset DOI: 10.5061/dryad.t1g1jwtfv
Repository: Dryad Digital Repository
License: Creative Commons Zero (CC0) Public Domain Dedication

Authors

Esaú Victor de Araújo¹², Mariana Valeria Haase³, Jorge Cubo³, Luiz Carlos Weinschütz⁴, Alexander Wilhelm Armin Kellner¹², Juliana Manso Sayão¹²

¹ Laboratório de Sistemática e Paleontologia de Vertebrados Fósseis (LAPUG), Departamento de Geologia e Paleontologia, Museu Nacional/Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
² Programa de Pós-graduação em Zoologia (PPGZoo), Museu Nacional/Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
³ Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS, Centre de Recherche en Paléontologie–Paris (CR2P, UMR 7207), Paris, France.
⁴ Centro Paleontológico (CENPALEO), Universidade do Contestado, Campus Mafra, Brazil.

Corresponding author: Esaú V. Araújo (esauvictor@ufrj.br)

Overview

This dataset contains phylogenetic, osteohistological, comparative physiological, and imaging data used to estimate resting metabolic rate (RMR) and maximum metabolic rate (MMR) in the tapejarid pterosaur Caiuajara dobruskii. The inferences are based on osteocyte lacunar density, relative primary osteon area, and nutrient foramen size, and were analyzed using phylogenetic eigenvector map (PEM) methods and ancestral character estimation (ACE).

The repository includes tab-delimited data tables, phylogenetic trees in Nexus format, R scripts used for comparative analyses and figure generation, a 3D segmented femur mesh in STL format, a ZIP archive of CT slice images, and supplementary files associated with the study.

Related study

We request that future users cite the associated article and this Dryad dataset when reusing these files:

Araújo, E.V., Sena, M.V.A., Cubo, J., Weinschütz, L.C., Kellner, A.W.A., & Sayão, J.M. (2025). Evidence for elevated metabolic rates in the tapejarid pterosaur Caiuajara dobruskii. Paleobiology. DOI pending at the time of dataset submission.

Complete file list

1. Ancrestal_state_analysis.R – R script for ancestral character estimation (ACE) of resting metabolic rate across the phylogeny.
2. humerusCPV1032.txt – Tab-delimited osteohistological dataset for Caiuajara dobruskii specimen CP.V 1032 and comparative taxa.
3. humerusCPV5698.txt – Tab-delimited osteohistological dataset for Caiuajara dobruskii specimen CP.V 5698 and comparative taxa.
4. MMRdata1.txt – Tab-delimited dataset used to infer mass-independent maximum metabolic rate (MMR).
5. phylotree_humerus.trees.nex – Phylogenetic tree used for humerus-based PEM analyses.
6. phylotree.trees_femur.nex – Phylogenetic tree used for femur-based PEM analyses.
7. phylotree.trees_MMR.nex – Phylogenetic tree used for MMR-based analyses.
8. phylotree.trees_tibia.nex – Phylogenetic tree used for tibia-based PEM analyses.
9. RMRdataCPV2057.txt – Tab-delimited resting metabolic rate (RMR) dataset associated with specimen CP.V 2057.
10. RMRdataCPV2058.txt – Tab-delimited resting metabolic rate (RMR) dataset associated with specimen CP.V 2058.
11. Script_7.RPtero_FEMUR.R – R script for PEM analysis of the femur dataset.
12. Script_7.RPtero_Humerus.R – R script for PEM analysis of the humerus dataset.
13. Script_7.RPtero_tibia.R – R script for PEM analysis of the tibia dataset.
14. Script_PEM_exp_087_1.R – R script for PEM analysis of the MMR dataset using a body-mass exponent of 0.87.
15. Script._Boxplot_analysis.R – R script used to generate the boxplot/stripchart visualization of mass-independent RMR.
16. Segmentation_Femur_CP.V8657.stl – 3D surface mesh of femur specimen CP.V 8657 generated from micro-CT data.
17. SLICES_-_FEMUR_CP.V8657.zip – ZIP archive of CT slice images documenting the femur CP.V 8657 tomographic dataset.
18. Supp_Figure_1.png – Supplementary Figure 1 showing mass-independent RMR of Caiuajara dobruskii relative to extant ectotherms and endotherms.
19. Supp_Table_1.pdf – Supplementary Table 1 containing RMR values for 22 extant species used to construct the mass-independent RMR inference model.
20. Supp_Table_2.pdf – Supplementary Table 2 containing the dataset used to infer mass-independent MMR in Caiuajara dobruskii.
21. tibiaCPV2059.txt – Tab-delimited osteohistological dataset for Caiuajara dobruskii specimen CP.V 2059 and comparative taxa.
22. tibiaCPV2750a.txt – Tab-delimited osteohistological dataset for Caiuajara dobruskii specimen CP.V 2750a and comparative taxa.
23. zscoreRMRdataCPV2057.txt – Tab-delimited calibration dataset and derived values used for z-score and linear-distance analyses of mass-independent RMR.

Files and variables

1. Osteohistological data tables

The files humerusCPV1032.txt, humerusCPV5698.txt, tibiaCPV2059.txt, and tibiaCPV2750a.txt are tab-delimited data tables used in PEM analyses of osteohistological correlates of metabolic rate.

These files contain the same type of information but correspond to different skeletal elements and/or specimens. Variable names should be reported exactly as they appear in each file. If a short code such as V0, V1, or V2 is used in a given table, its meaning should be interpreted according to the table below and checked directly against the file header.

Additional notes for these files:

• Values are tab-delimited plain text.
• Missing values are coded as NA.
• OLD values are osteohistological measurements derived from bone thin sections.
• RPOA means relative primary osteon area.
• Where a script applies transformation or scaling to any of these variables, the transformed values are calculated from the variables listed above rather than stored as separate raw measurements unless explicitly indicated in the table.

2. MMR data table

MMRdata1.txt is a tab-delimited table used to infer mass-independent maximum metabolic rate (MMR) in Caiuajara dobruskii.

Additional notes:

• This file underlies the inference of mass-independent MMR in the fossil taxon.
• Measurements are provided as tab-delimited values.
• The body-mass exponent applied in the associated script is 0.87.
• If a transformed variable is included in the file, it is used to generate the mass-independent estimate reported in the manuscript.

3. Raw RMR data tables

RMRdataCPV2057.txt and RMRdataCPV2058.txt contain resting metabolic rate calibration data associated with the femur-based analyses.

Additional notes:

• These files are raw comparative/calibration tables linked to the femur-based RMR analyses.
• They contain the data used to estimate the fossil value for Caiuajara dobruskii specimen CP.V 2057 or CP.V 2058.
• Missing values are coded as NA.

4. Z-score calibration table

zscoreRMRdataCPV2057.txt is a tab-delimited table containing the RMR calibration dataset and derived values used for z-score and linear-distance analyses.

Additional notes:

• This file is used by Script._Boxplot_analysis.R.
• The figure associated with this file expresses mass-independent RMR as mL O2 h-1 g^-0.86.
• The file combines comparative extant values with the inferred fossil estimate used in the supplementary figure.

5. Phylogenetic tree files

The files phylotree_humerus.trees.nex, phylotree.trees_femur.nex, phylotree.trees_MMR.nex, and phylotree.trees_tibia.nex are phylogenetic trees in Nexus format.

These files include:

• the taxon names used in the PEM and ACE analyses;
• the topology required for phylogenetic comparative methods; and
• the branch-length information used by the corresponding R scripts.

6. R scripts

The R scripts are provided as reproducible analytical workflows. They are listed below with their main purpose, expected input files, and main output or analytical result. These descriptions are intended to help users understand the workflow without needing to read R code.

File: Ancrestal_state_analysis.R

• Description: Performs ancestral character estimation (ACE) of resting metabolic rate across the phylogeny. The script uses a phylogenetic tree and comparative RMR data to reconstruct estimated ancestral values at internal nodes and to generate the ancestral-state figure used to interpret evolutionary patterns in metabolic physiology.
• Main input files: Phylogenetic tree file and comparative RMR dataset used by the script
• Main output or use: Ancestral-state reconstruction output and figure.

File: Script_7.RPtero_FEMUR.R

• Description: Runs the phylogenetic eigenvector map (PEM) analysis for the femur-based osteohistological dataset. The script reads the femur data table and the corresponding phylogenetic tree, fits the comparative model, and generates the femur-based metabolic-rate inference for Caiuajara dobruskii.
• Main input files: Femur data table(s), phylotree.trees_femur.nex
• Main output or use: Femur-based inferred RMR values and model output used in the manuscript.

File: Script_7.RPtero_Humerus.R

• Description: Runs the PEM analysis for the humerus-based osteohistological dataset. The script links humeral osteohistological variables with comparative physiological data in a phylogenetic framework in order to estimate metabolic parameters for the fossil taxon.
• Main input files: humerusCPV1032.txt, humerusCPV5698.txt, phylotree_humerus.trees.nex
• Main output or use: Humerus-based model results and inferred metabolic values.

File: Script_7.RPtero_tibia.R

• Description: Runs the PEM analysis for the tibia-based osteohistological dataset. The script uses tibial histological measurements and the tibia phylogeny to estimate fossil metabolic parameters within the comparative dataset.
• Main input files: tibiaCPV2059.txt, tibiaCPV2750a.txt, phylotree.trees_tibia.nex
• Main output or use: Tibia-based model results and inferred metabolic values.

File: Script_PEM_exp_087_1.R

• Description: Runs the PEM analysis for maximum metabolic rate (MMR) using a body-mass exponent of 0.87. The script uses nutrient foramen measurements and comparative physiological data to estimate mass-independent MMR in Caiuajara dobruskii.
• Main input files: MMRdata1.txt, phylotree.trees_MMR.nex
• Main output or use: Inferred mass-independent MMR estimate and comparative model output.

File: Script._Boxplot_analysis.R

• Description: Reads the RMR calibration table and generates the supplementary boxplot/stripchart comparing mass-independent RMR values of extant ectotherms, extant endotherms, and the inferred value for Caiuajara dobruskii. The script also summarizes the comparative distributions used to position the fossil estimate relative to living taxa.
• Main input files: zscoreRMRdataCPV2057.txt
• Main output or use: Supplementary figure showing the distribution of mass-independent RMR values and the fossil estimate.

General script notes:

• Scripts are provided as runnable analytical workflows.
• Users may need to set the working directory to the folder containing the data files.
• Some scripts require editing file paths before execution, depending on the local environment.
• Any data transformations used in a script, such as mass correction, z-score calculation, or ancestral-state inference, should be interpreted together with the corresponding input data table described in this README.

7. 3D and tomographic files

Recommended software for viewing:

• MeshLab
• Blender
• Avizo
• VGStudio
• Other standard CT or mesh-visualization software

8. Supplementary files

Data relationships

The tabular data files provide the measured or compiled variables used as input for comparative analyses. The Nexus files provide the phylogenetic framework required for PEM and ACE analyses. The R scripts connect these inputs to the analytical outputs, including metabolic-rate estimates, boxplot visualizations, and ancestral-state reconstructions.

The STL mesh and CT slice archive document the anatomical basis of the nutrient foramen measurements used in the MMR component of the study. The supplementary figure and tables provide visual and tabular support for the results presented in the manuscript.

Software requirements

Required for analysis

• R version 4.0 or later
• R packages: MPSEM, phytools, ape, ggplot2

Optional for 3D visualization

• MeshLab
• Blender
• Avizo
• VGStudio

Original acquisition/segmentation environment

• Zeiss Xradia 510 Versa
• Mimics Innovation Suite v24

Data format and standards

• Text tables are UTF-8 encoded.
• Delimited text files can be opened in any text editor, spreadsheet program, or statistical environment.
• Missing data are indicated by NA.
• Nexus files follow standard phylogenetic tree formatting.
• STL files are polygon mesh files for 3D visualization.
• ZIP files contain image-based tomographic slices.

Abbreviations

Usage notes

To reproduce the analyses, place the data tables, tree files, and scripts in the same working directory or edit the file paths in each R script accordingly. Users should verify the exact column names in each data file before rerunning analyses, especially in files where variables are represented by generic labels such as V0–V6.

The fossil physiological values in this dataset are inferred from comparative models and should not be interpreted as directly measured metabolic rates. The 3D and CT-based files can also be reused for anatomical visualization, remeasurement of the nutrient foramen, or independent morphometric and biomechanical analyses.

Access information

Some comparative frameworks used in this dataset were derived from previously published sources, including:

Cubo, J., Sena, M. V. A., Pellarin, R., Faure-Brac, M. G., Aubier, P., Cheyron, C., Jouve, S., Allain, R., & Jalil, N.-E. (2025). Integrative paleophysiology of the metriorhynchoid Pelagosaurus typus (Pseudosuchia, Thalattosuchia). The Anatomical Record, 308(2), 394–411. https://doi.org/10.1002/ar.25548

License

This dataset is distributed under the Creative Commons Zero (CC0) Public Domain Dedication.

Preferred citation

If this dataset is reused, we request that you cite both the associated article and the Dryad dataset record.