DOI: 10.5061/dryad.m905qfvb8
title: Data from: For a while, crocodile: crocodylomorph resilience to mass extinctions

description: Crocodylomorphs are the sole survivors of the pseudosuchian clade and
 have, thus far, endured two mass extinctions. Despite being stereotyped as
 “living fossils”, the characteristics that facilitated their survival
 remain largely unknown, but trends in other clades, such as mammals,
 suggest that dietary ecology may play a key role in persisting during and
 after mass extinctions. To test the role of dietary ecology in the
 survival of crocodylomorphs, we use geometric and linear morphometrics to
 quantify the cranial shape of crocodylomorphs through the Mesozoic and
 into the Cenozoic. We then compare these data to living amniotes and
 combine these results with additional morphological proxies, which
 together permit the reconstruction of dietary ecology. We find that
 crocodylomorph cranial morphology exhibits a greater disparity during much
 of the Mesozoic than today. Many extinct crocodylomorphs express
 morphologies that overlap with extant crocodylians and lepidosaurs,
 indicating a diverse range of diets, but convergence with extant mammals
 is exceptionally rare. Numerous crocodylomorphs from across geologic time
 and phylogeny span a range of morphospace not occupied by sampled extant
 amniotes. Using these data, we suggest that a generalist dietary ecology
 is associated with mass extinction survivors, a trend previously observed
 in other clades, such as mammals. Terrestrial generalists appear to
 survive and diversify following the end-Triassic mass extinction, whereas
 semiaquatic generalists persist through the end-Cretaceous mass
 extinction. We propose that one reason for the success and longevity of
 the crocodylomorph clade is their remarkable dietary flexibility, a
 characteristic that is still observed in living crocodylians.
description: Photography of skulls in dorsal and lateral view, as well as raw
 landmark data derived from ImageJ.
description: # Data from: For a while, crocodile: crocodylomorph resilience to mass
 extinctions
 [https://doi.org/10.5061/dryad.m905qfvb8](https://doi.org/10.5061/dryad.m905qfvb8) ## Description of the data and file structure This dataset contains 2D photos of the entire dataset of extinct crocodylomorphs in dorsal and lateral view. Additionally, the comparative extant dataset of mammal, crocodylian, and lipidosaur photographs (also in dorsal and lateral view) originally published in Melstrom et al. (2021) are included. All 2D landmark coordinates in lateral and dorsal views derived from FIJI landmarking as well as accompanying .csv files with additional data (clades, ages, and ecology), .nex files, and FAD LAD (i.e., first appearance datum; last appearance datum) files are located in .zip files. An additional .zip file contains only crocodylomorph landmark data used for Procrustes disparity analyses. The single R script to run geometric morphometric and disparity analyses is included. A final R script and two .csv files needed to perform linear morphometric analyses are located in a .zip file. ### Files and variables #### File: Extinct\_Crocodylomorph\_GM\_analyses\_Dryad.R **Description:** This R file contains all scripts used to run geometric morphometric, PCA, and disparity analyses for the dorsal and lateral datasets. It uses .txt landmark files, generated from FIJI, to run geometric morphometric analyses. Additional .csv files (included in .zip files) were created from combined R PCA outputs and information on ecology (including diet for extant taxa), clade, and age (for extinct taxa). If new analyses are run, these .csv files will need to be updated with the new PCA data.  #### File: Croc\_Only\_Procrustes\_disparity\_dorsal.zip **Description:** This group of files contains all landmark data of extant and extinct crocodylomorphs investigated in this study. All .txt files (738 separate documents) have been generated in FIJI and are landmark data. Files with \_LM are landmarks, \_R are ruler points representing 1 cm, and \_C1, \_C2, \_C3, and \_C4 are semi landmark curves made using the Bezier curve tool. It is to be used for Procrustes Disparity measurements in the Geomorph R package. Three .csv files (pcaDisparity.procrustes.csv, LateralGPA_2D_fulldataset.csv, pcaDisparity.geomorph.csv) document PCA and GPA results, as well as additional columns includes age, diet, and taxon information tied to GPA results. 21.7 mb. #### File: Extinct\_and\_Extant\_Dorsal\_View\.zip **Description:** A group of files containing all landmark data (1,554 .txt files) for the extinct and extant skulls in dorsal view used for this analysis. File names include species and genus, the specimen number, indicator of general clade (C for crocodylian, EC for extinct crocodylomorph, M for mammal, L for lizard, and S for *Sphenodon*), and signal for type of landmark data (C1–4 for semi landmark curve, LM for landmark, R for ruler). We include several .CSV files that were generated and are needed for plots (Info_and_PCA2.csv) and dispaRity analyses (CrocGPA_pruned.csv) are also included. .CSV files that are raw PCA output data (pcaFull.geomorph.csv) were subsequently edited to add clear names (column 1), taxonomic groups used for the study (i.e., extant crocodylian, fossil crocodylomorph, mammal, squamate, and rhynchocephalian) (2), Order/suborder (3), Family/subfamily (4), diet (5), detailed diet (not used in final study) (6), locomotor ecology (7), Age of specimen, increasing in specificity (8–10), numerical key to use to easily ID specimens on plot, and PC data (all subsequent columns). The file Info_and_PCA2.csv was the primary file used to generate all plots, with other .CSV files being used to generate that data or were previous versions. To investigate disparity through time, a GPA dataset was exported (CrocGPA.csv), edited (CrocGPA_pruned.csv) to match names with phylogenetic data. An initial phylogenetic tree was made in Mesquite, exported as .nex (Crocodylomorph phylogeny.trees.nex), uploaded to R, which was subsequently used to write a new .tree file (CrocTree). FAD LAD data were linked to this file using the .CSV file CrocOnly_Dorsal_FAD_LAD.csv. Files that end with .R1 (CrocAges.R1, CrocOnly_Dorsal_FAD_LAD_R1.csv) modify taxa known from the Adamantina Formation to have new FAD LAD dates of 83.5 and 66, respectively. 25.5 mb. #### File: Extinct\_and\_Extant\_Lateral\_View\.zip **Description:** A group of .txt files (1,160 in total) containing all landmark data for the extinct and extant skulls in lateral view used for this analysis. File naming scheme follows dorsal dataset, but with "Lateral" included. Additional .csv files (e.g., pcaLateralTogether.csv) are included as well. The file pcaLateral.geomorph.csv is the raw PCA data, whereas pcaLateralTogether.csv is the edited file with clear names (column 1), taxonomic groups (i.e., extant crocodylian, fossil crocodylomorph, mammal, squamate, and rhynchocephalian) (2), Order/suborder (3), Family/subfamily (4), diet (5), locomotor ecology (6), Age of specimen (7), and PCA information (subsequent columns) 14.5 mb. #### File: Skull\_Photos.zip **Description:** JPG files of all specimens used in these analyses in dorsal and lateral view. 1.77 gb. #### File: Linear Morphometrics.zip **Description:** One R file (Linear Morphometrics dataset.R) and two .csv files that run linear morphometric analyses. These .csv files are designed to work directly with the R script, but also include some blank columns and additional notes (explained below). One .csv file (Melstrom et al. Dataset_Extant.csv) contains all the extant data whereas the second has the extinct data (Melstrom et al. Dataset_Extinct). The extant CSV file includes columns for the file name that allows for comparisons with Geometric Morphometric analyses (1), taxonomic groups (i.e., extant crocodylian, fossil crocodylomorph, mammal, squamate, and rhynchocephalian) (2), Order/suborder (3), Family/subfamily (4), genus (5), species (6), the common name (7), specimen number (8), diet (9), locomotor ecology (10) and cranial measurements (described in detail in the publication) (11–20). Additional detailed information on diet including key references is included in column 21, with secondary notes in column 22, and a blank column to separate raw data from sized normalized data for column 23. Linear morphometric analyses are conducted on size-normalized data (columns 24–32). The Melstrom et al. Dataset_Extinct file includes columns for taxon names (1), clade (2), cranial measurements (3–12), diet (13), locomotor ecology (14), and cranial measurements normalized by total skull length (columns 16–24). An additional column with blank cells are include (column 15) to separate raw measurements from normalized measurements. All cranial measurements that have not been normalized are in mm. ## Code/software The R statistical software is needed to view and run the included R scripts (Extinct Crocodylomorph GM analyses.R, LinearMorphometrics.R). Mesquite ([http://www.mesquiteproject.org](http://www.mesquiteproject.org)) was used to originally build NEXUS files and can be used to view and edit files.