DOI: 10.5061/dryad.73n5tb3bc
title: Data from: Decoupled diversity and disparity after faunistic turnover in caviomorph rodents

description: 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.
description: # Data from: Decoupled diversity and disparity after faunistic turnover
 in caviomorph rodents Dataset DOI:
 [10.5061/dryad.73n5tb3bc](https://doi.org/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\ \&gt; matrix_mapker.py\ \&gt; raxml analyses\
 \&gt; Root age calibration\ \&gt;
 supermatrix_filt_clean_mt-nuc_wdummy_20221003.nex\ \&gt;
 supermatrix_moleculardata_only.nex\ \&gt; Time-calibrated phylogeny\ \-
 **Dataset S4** - Body mass evolution analyses\ \&gt; Body mass evolution
 plots.R\ \&gt; clade_partitions.txt\ \&gt; FossilBM_input_files\ \&gt;
 FossilBM_output_files\ \&gt; fossilBM-dev\ \&gt; plot_data_BS_notrend.txt\
 \&gt; plot_data_BS_trend.txt\ \&gt; Rates of Body size evolution\ \&gt;
 temp.log\ \- **Dataset S5** - Diversity through time\ \&gt; DeepDive
 diversity estimates\ \&gt; LTT diversity\ \- **Dataset S6** - Morphospace
 extant\ \&gt; MCC_tree.tre\ \&gt; Measurements_PCA.txt\ \&gt;
 Phylomorphospace.R\ \- **Dataset S7** - Disparity through time \&gt;
 caviomorphs_matrix_for_Claddis.nex\ \&gt; caviomorphs_matrix.nex\ \&gt;
 Disparity caviomorphs.R\ \&gt; matrix_no_inapplicable_for_Claddis.nex\
 \&gt; 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/](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](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/](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](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](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](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/](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](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](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](https://paleobiodb.org))