Data from: Decoupled diversity and disparity after faunistic turnover in caviomorph rodents
Data files
Jan 14, 2026 version files 1.05 GB
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Data_from_Carrillo_et_al_Caviomorphs.zip
1.05 GB
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README.md
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Abstract
Caviomorph rodents diversified widely in the Americas. Within this group, the sister clades Octodontoidea (spiny rats and allies) and Chinchilloidea (chinchillas and allies) illustrate strikingly imbalanced evolution, with 195 extant species in the former and only six in the latter. Fossil evidence, however, documents greater past diversity and disparity in Chinchilloidea, including the largest known rodents. Here, we integrate data from extant and extinct species to investigate how evolutionary dynamics shaped these contrasting trajectories. Using a phylogenetic framework, we reconstructed patterns of body mass and craniodental evolution. The ancestral body mass was small, but Chinchilloidea expanded into a broader size range, showing significantly higher rates of body mass evolution than Octodontoidea. Subsequent Neogene and Quaternary extinctions erased much of this variation, reversing a ~30-million-year trend of greater body mass disparity. Craniodental disparity, however, followed a different trajectory: initially higher in Chinchilloidea, it later became greater in Octodontoidea after the Miocene. Importantly, craniodental disparity remained relatively stable in both clades despite major diversification and extinction events. These findings highlight the decoupling of taxonomic diversity, body mass, and craniodental morphology, underscoring the complexity of evolutionary dynamics even for sister clades that evolved on the same continent.
Dataset DOI: 10.5061/dryad.73n5tb3bc
Description of the data and file structure
This repository contains the datasets and scripts associated with the study of body mass, cranial morphology, phylogeny, diversity, and disparity in Chinchilloidea and Octodontoidea. Each dataset corresponds to the analyses presented in the manuscript and supplementary materials.
Files and variables
File: Data_from_Carrillo_et_al_Caviomorphs.zip
The folder structure of Data_from_Carrillo_etal_Caviomorphs.zip is as follows:
Data_from_Carrillo_etal_Caviomorphs.zip
- Dataset S1.xlsx
- Dataset S2 Traits_table.xlsx
- Dataset S3 - Phylogenetic analyses data and code
> matrix_mapker.py
> raxml analyses
> Root age calibration
> supermatrix_filt_clean_mt-nuc_wdummy_20221003.nex
> supermatrix_moleculardata_only.nex
> Time-calibrated phylogeny
- Dataset S4 - Body mass evolution analyses
> Body mass evolution plots.R
> clade_partitions.txt
> FossilBM_input_files
> FossilBM_output_files
> fossilBM-dev
> plot_data_BS_notrend.txt
> plot_data_BS_trend.txt
> Rates of Body size evolution
> temp.log
- Dataset S5 - Diversity through time
> DeepDive diversity estimates
> LTT diversity
- Dataset S6 - Morphospace extant
> MCC_tree.tre
> Measurements_PCA.txt
> Phylomorphospace.R
- Dataset S7 - Disparity through time
> caviomorphs_matrix_for_Claddis.nex
> caviomorphs_matrix.nex
> Disparity caviomorphs.R
> matrix_no_inapplicable_for_Claddis.nex
> taxa_ages.txt
Description:
Dataset S1 – Craniodental traits of extant species:
Spreadsheet with the craniodental measurements for extant Chinchilloidea and Octodontoidea. Measurement abbreviations correspond to Figure 3 and Table S1 of the manuscript. Values are in millimeters (mm). IDAS = individual dental ages; NA = measurement not available.
Dataset S2 – Body mass and cranial traits in extinct and extant species:
Spreadsheet with the body mass data for extant and extinct Chinchilloidea and Octodontoidea (Tables S5–S6 of the manuscript), along with species-level averages of craniodental measurements for extant taxa. Measurement abbreviations follow Figure 3 and Table S1 of the manuscript. Units in millimeters (mm). Empty cells represent data were not measured. The abbreviations are as follows:
- R – Length of the tooth row
- WM – Mean tooth width
- WZ – Width of the zygomatic region
- BL – Basal length of the skull or mandible
- Wmax – Maximum width
- PPL – Palatal length (post-palatal length)
- HB – Height of the braincase
- HZP – Height of the zygomatic plate
Dataset S3 – Time-calibrated phylogenetic analysis:
This folder contains the Nexus and XML files containing the molecular and morphological datasets used in phylogenetic analyses. It also includes an annotated Python script for concatenating mitochondrial and nuclear sequences, and annotated R scripts for estimating the age of origin of Octochinchilloi (Chinchilloidea + Octodontoidea) using the Bayesian Brownian Bridge (BBB) model.
matrix_mapker.py: Annotated Python script for concatenating mitochondrial and nuclear sequences
raxml analyses: This folder contains the files used to run the maximum likelihood phylogenetic analysis of the extant Chinchilloidea and Octontoidea based on molecular data only.
Input and output files of the raxmlGUI 2.0 analyses: https://antonellilab.github.io/raxmlGUI/
Input files for raxmlGUI 2.0:
molecular_supermatrix.txt : Input file with the molecular super matrix
Partitions files
16_partitions.txt : Input file with the 16 partitions identified by PartitionFinder2
1_partitions.txt : Input file with 1 partition
Output files:
molecular_supermatrix.raxml.support_1_part.tre : Consensus tree of analysis using 1 partition
molecular_supermatrix.raxml.support_16_part.tre : Consensus tree of analysis using 16 partitions
Root age calibration: This folder contains the input and output files, as well as the annotated R code used to estimate the age of origin of the Octochinchilloi clade using the Bayesiarn Brownian Bridge (BBB) model: https://github.com/dsilvestro/rootBBB
Age ranges fossils.txt : Text file with the age range information of each species
Caviomorph_BBB_logfiles: output files of the BBB analysis
Clade_diversity.txt : Text file with the information of the current species diversity of the clade for each replicate
Counts_fossils.txt : Text file with the number of fossil occurrences for each species for each replicate
Root calibration script.R : Annotated R script used to generate the BBB input files and read the BBB output files
supermatrix_filt_clean_mt-nuc_wdummy_20221003.nex : Matrix with molecular data including extant and extinct (without data) taxa.
supermatrix_moleculardata_only.nex : Matrix with molecular data including extant taxa only.
Time-calibrated phylogeny : This folder contains the input and output files of the time calibrated Bayesian phylogenetic analysis using BEAST2 v.2.6.7: https://www.beast2.org/
Constraints_1part_relax_morpho_clock_bounded_v2_constraints_edited.xml: xml input file for BEAST
Fig S3_290824.tiff : Figure showing the Maximum clade credibility tree of the phylogenetic relationships of extinct and extant Chinchilloidea (Fig. S3 in the manuscript)
MCC_tree_290824.tree: Tree file with the Maximum clade credibility tree
Plot_MCC_tree.R: Annotated R script to produce the Fig. S3
Dataset S4 – Analyses of body mass evolution:
This folder includes the input and output files used in Bayesian analyses of body mass evolution, including post-burn-in trees and files/code from the fossilBM program:https://github.com/dsilvestro/fossilBM
It also includes the annotated R scripts to calculate and plot evolutionary rates for both clades.
Body mass evolution plots.R : Annotated R scripts to read the fossilBM output files and calculate and plot evolutionary rates of body mass evolution
clade_partitions.txt: Text file indicating the taxonomic partitions for fossilBM
FossilBM_input_files: FossilBM input text files
FossilBM_output_files: FossilBM output log files
fossilBM-dev: the fossilBM program downloaded from: https://github.com/dsilvestro/fossilBM
plot_data_BS_notrend.txt: text file with the evolutionary rates for the analysis without a trend parameter
plot_data_BS_trend.txt : text file with the evolutionary rates for the analysis with a trend parameter
Rates of Body size evolution: This folder contains the log files and annotated R script to generate the plots of the evolutionary rates of body mass evolution
temp.log: .log file indicating the taxonomic partitions for fossilBM
Dataset S5 – Diversity through time:
This folder contains the fossil occurrence data for extinct Chinchilloidea and Octodontoidea with references, plus input files and an annotated R script for estimating diversity through time using DeepDive. It also includes trees and scripts used to obtain lineage-through-time (LTT) diversity curves.
DeepDive diversity estimates : This folder contains the input and output files as well as the annotated R scripts used in the diversity through time analysis usint DeepDive: https://github.com/DeepDive-project
Areas DeepDive.txt: Text file providing the biogegraphic areas used in the analysis
Cavi_DD_plots.R: Annotated R script to read and plot the output files obtained from the DeepDive analysis
cavio_res : This folder contains the trained DeepDive models
Chinchilloidea_dd.xlsx : Spreadsheet with the Chinchilloidea DeepDive estimate diversity results
chinchilloidea.ini : Text file describing Chinchilloidea input parameters
DeepDive Chin input.R : Annotated R script to generate Chinchilloidea DeepDive input files
DeepDive Oct input.R : Annotated R script to generate Octodontoidea DeepDive input files
deepdive_input_chinchilloidea.csv : csv file with DeepDive Chinchilloidea input data
deepdive_input_octodontoidea.csv : csv file with DeepDive Octodontoidea input data
Octodontoidea_dd.xlsx: Spreadsheet with the Octodontoidea DeepDive estimate diversity results
octodontoidea.ini : Text file describing Octodontoidea input parameters
LTT diversity : This folder contains the tree files and annotated R script used to generate the Lineage Through Time (LTT) diversity
LTTplots.R : Annotated R script to generate the Lineage Through Time (LTT) diversity
Trees_Chinchilloidea.tree : Chinchilloidea tree files
Trees_Octodontoidea.tree : Octodontoidea tree files
Dataset S6 – Morphospace occupation of extant species:
This folder contains the files and annotated R script used to compute the phylomorphospace of extant Chinchilloidea and Octodontoidea and to compare morphospace occupation while accounting for differences in species richness.
MCC_tree.tre : Tree file with the maximum clade credibility tree
Measurements_PCA.txt : Text file with the cranial measurements used for the PCA
Phylomorphospace.R : Annotated R script used to compute the phylomorphospace of extant Chinchilloidea and Octodontoidea
Dataset S7 – Craniodental disparity through time:
This folder contains the files and annotated R script used to estimate craniodental disparity through time for extinct and extant Chinchilloidea and Octodontoidea based on the taxon–character matrix.
caviomorphs_matrix_for_Claddis.nex : Morphological character matrix used for the disparity analysis
caviomorphs_matrix.nex : Unedited morphological character matrix
Disparity caviomorphs.R : Annotated R script used to estimate craniodental disparity through time
matrix_no_inapplicable_for_Claddis.nex : Morphological character matrix excluding the innaplicable characters used for the disparity analysis
taxa_ages.txt : Text file with the age range information of each species
Code/software
All analyses were conducted using free and open-source software. Below we provide the software requirements, version information, loaded packages, and a brief description of the workflow. All scripts included in the repository are annotated and correspond directly to the analyses described in the manuscript.
Phylogenetic analyses
- BEAST2 v2.6.7 was used for the total-evidence time-calibrated phylogenetic analysis. https://www.beast2.org/
- Required packages: SA package, BEASTLabs, BDSS, and Tracer v1.7.2 for assessing MCMC convergence.
- XML input files were generated using BEAUti (distributed with BEAST2).
- Output log and tree files can be viewed with Tracer and TreeAnnotator.
Bayesian body-mass evolution analyses
- fossilBM was used to infer evolutionary rate, trend, and ancestral states. https://github.com/dsilvestro/fossilBM
Morphological disparity analyses
- Conducted in R v4.3.x with the following CRAN packages:
- Claddis v0.7
- dispRity v1.7.0
- FactoMineR v2.9
- phytools v1.7
- ape v5.8
Phylomorphospace construction
- Performed in R, using phytools and FactoMineR.
Diversity-through-time analyses
- Conducted using DeepDive https://github.com/DeepDive-project
- Neural-network models were configured using DeepDiveR (R package v1.0).
Each folder. contains all the input and output files, as well as the associated code explaining input requirements.
Access information
Fossil occurrence data of Octochinchilloi caviomorphs used in the DeepDive analysis, was obtained from the Paleobiology Database (https://paleobiodb.org)
