DOI: 10.5061/dryad.qfttdz0p5
title: Data from: Limited convergence in the postcranium of aquatic crocodylomorpha

description: Thalattosuchia (Early Jurassic–Early Cretaceous) and Dyrosauridea (Late
 Cretaceous–Early Eocene) are crocodylomorph archosaurs which
 diversified in fluvial and marine environments and endured extinction
 events (i.e. Jurassic–Cretaceous boundary for Thalattosuchia;
 Cretaceous–Paleogene for Dyrosauridea). Their postcrania remain
 globally undervalued in anatomical descriptions and diagnoses, shrouding
 the locomotive adaptations that possibly underpinned their radiations and
 longevity. We thoroughly surveyed the postcranial morphology of
 Dyrosauridea and Thalattosuchia, recreated their girdles in
 three-dimensions using tens of high-precisions 3D scans, and
 analysed their shape using geometric morphometrics.
 Dyrosauridea and Thalattosuchia have clearly distinct postcrania,
 even when found within similar environments, suggesting the existence of
 clade-specific features limiting the strength of evolutionary convergence.
 Moreover, the range of postcranial morphologies evolved by
 dyrosaurids and thalattosuchians is large compared to
 extant crocodylians, making the latter unsatisfactory functional
 analogues for every group of extinct crocodylomorphs. Our work reveals the
 previously unsuspected potential of postcranial anatomy as an abundant
 source of phylogenetic and taxonomic characters to assess the
 relationships within Crocodylomorpha. Incorporation of
 postcranial anatomy therefore appears crucial to fully assess the ecology,
 disparity, and relationships of crocodylomorphs.
description: This dataset contains: the
 supplementary information of the article 'Limited convergence in the
 postcranium of aquatic crocodylomorpha' all the
 repaired 3D models (original raw scans can be found on
 Morphosource) all the landmark coordinates
 all the R scripts to run the different analyses
description: R scripts require the free statistical software
 R 3D models are PLY and can be viewed with a variety
 of softwares Landmark coordinates were originally
 taken with Checkpoint Stratovan
description: # Data from: Limited convergence in the postcranium of aquatic
 crocodylomorpha *** ## Description of the Data and file structure
 Morphosource contains the original raw meshes (modeled from laser or
 white-light scans) The datasets uploaded on Dryad and ORBi contain: * the
 supplementary information of the article 'LIMITED CONVERGENCE IN THE
 POSTCRANIUM OF AQUATIC CROCODYLOMORPHA'; * all the repaired 3D models
 (original raw scans can be found on Morphosource) * all the landmark
 coordinates * all the R scripts to run the different analyses Detailed
 decription of the files: * Models.7z comprises all our repaired 3D models
 with their landmark coordinates and corresponding sliders.csv file used in
 the landmark analysis from the Code.R and Code\_LandmarkCombine\_updated.r
 scripts. Models.7z contains bone folders named after each bone used in our
 analyses: Coracoid, Femur\_outline, Humerus, Ilium, Ischium, Pubis,
 Scapula (***XXX***), plus a *Combined* folder. The *Combined* folder
 comprises three additional subfolders (Pelvic, Thoracic and Total), which
 in turn contain corresponding bone folders (Femur, Ilium, Ischium, Pubis
 for Pelvic; Coracoid, Humerus, Scapula for Thoracic; and Femur, Ilium,
 Ischium, Pubis, Coracoid, Humerus, Scapula for Total). * Each bone
 ***XXX*** subfolder contains: \-\- a series of **.PLY** files which
 correspond to the 3D models. The filenames contain information on species
 and inventory number. \-\- a series of **.PLY.CKPT** files which are
 Checkpoint Stratovan save files. The filenames match the **.PLY** files.
 \-\- a series of **.PTS** files which contain all landmark coordinates .
 The filenames match the **.PLY** files. \-\- the phylomorphospaces
 constructed with the two first components of the PCA analyses
 \(**PCA\_*XXX*\_Repaired.PDF** and **PCA\_*XXX*\_Scaled.PDF** in which the
 axes are scaled to one another). \-\- a **sliders.CSV** file which is used
 in the R script **LandMarkTestCombine.R** to perform the General
 Procrustes Analysis on semi-landmarks. * ThalattoONLY.7z is a subsample of
 our dataset centered on Thalattosuchia only; it was used in the isolated
 Kmult analysis. It contains all necessary models and code: *
 **CodeThalattoONLY.R** which is a R script to run our different analyses
 (PCA on landmarks, phylomorphospace, ANOVA, Kmult, Mantel) on the reduced
 dataset comprising only thalattosuchians. This code does not combine the
 landmarks of different bones. * **Landmark\_Phylomorpho** folder contains
 * **LandMarkTestCombine.r** which is a R script to run our combined
 analyses (combination of different bone landmarks, PCA, ANOVA, Mantel,
 phylomorphospace) * **CSV files FAD\_LAD\_*XXX*.csv** each file contains
 the type of bone in its filename (*i.e.* replace *XXX* with Coracoid,
 Femur\_outline, Humerus, Ilium, Ischium, Pubis, Scapula) * First column
 contains the taxa list * Second column contains the first occurrence in
 m.y. * Third column contains the last occurrence in m.y. * **CSV files
 Bone\_convert\_*XXX*.csv** each file contains the type of bone in its
 filename (*i.e.* replace *XXX* with Coracoid, Femur\_outline, Humerus,
 Ilium, Ischium, Pubis, Scapula) * First column contains the list of taxa
 as it appears in the phylogenetic dataset * Second column contains the
 list of taxa with the filename corresponding to each 3D model * **Models**
 folder contains * Bone subfolders named after each bone used in our
 analyses: Coracoid, Femur\_outline, Humerus, Ilium, Ischium, Pubis,
 Scapula (***XXX***). * Each ***XXX*** subfolder contains \-\- a series of
 **.PLY** files which correspond to the 3D models. The filenames contain
 information on species and inventory number. \-\- a series of
 **.PLY.CKPT** files which are Checkpoint Stratovan save files. The
 filenames match the **.PLY** files. \-\- a series of **.PTS** files which
 contain all landmark coordinates . The filenames match the **.PLY** files.
 \-\- the phylomorphospaces constructed with the two first components of
 the PCA analyses \(**PCA\_*XXX*\_Repaired.PDF** and
 **PCA\_*XXX*\_Scaled.PDF** in which the axes are scaled to one another).
 \-\- a ***XXX*\_PCA.CSV** file in which the first column contains the list
 of each individual (which includes the bone type plus the species name or
 inventory number), and the columns starting from second through the last
 one contain the result of each component of the PCA analysis (*e.g.*
 Comp1, Comp2, Comp3, etc.). \-\- a **sliders.CSV** file which is used in
 the R script **LandMarkTestCombine.R** to perform the General Procrustes
 Analysis on semi-landmarks \-\- a nexus file ***XXX*.nex** which
 corresponds to the new tree built from the dataset of Jouve &
 Jalil 2020 to match our taxa list. This tree is built within the R script
 **LandMarkTestCombine.R** then it is exported. \-\- a
 ***XXX*\_timescale.PDF** file which is a timescaled representation of the
 new tree built to match our taxa list. It is built within the R script
 **LandMarkTestCombine.R** then it is exported. * R-code.zip folder
 contains: * **Code.R** which is a R script to run our different analyses
 (PCA on landmarks, phylomorphospace, ANOVA, Kmult, Mantel) *
 **Code\_LandmarkCombine\_updated.r** which is a R script to run our
 combined analyses (combination of different bone landmarks, PCA, ANOVA,
 Mantel, phylomorphospace) * **Convergence.R** which is a R script to run
 the updated Stayton convergence analysis (Ct metrics) * Phenogram.zip
 contains all necessary tables and script to build our humerus phenogram
 graphs. It contains: * **BonePhenogram\_code.R** which is the R script to
 build the phenogram graphs * **Variable description of CSV file
 Humerus\_Dyro\_Ratio.csv** * First column contains the list of dyrosaurid
 taxa * Second column contains the values of the humeral ratio (length over
 mid-width) * **Variable description of CSV file
 Humerus\_Thalatto\_Ratio.csv** * First column contains the list of
 thalattosuchian taxa * Second column contains the values of the humeral
 ratio (length over mid-width) * **Variable description of CSV file
 FAD\_LAD\_Humerus\_Thalatto.csv** * First column contains the list of
 thalattosuchian taxa * Second column contains the first occurrence in m.y.
 * Third column contains the last occurrence in m.y. * **Variable
 description of CSV file FAD\_LAD\_Humerus\_Dyro.csv** * First column
 contains the list of dyrosaurid taxa * Second column contains the first
 occurrence in m.y. * Third column contains the last occurrence in m.y. *
 Convergence\_Pairs.zip contains all necessary tables (list of taxa pairs
 and according PCA results in CSV) to run the updated Stayton convergence
 analysis (Ct metrics) from the Convergence.R script. It contains: *
 **Description of FigSX\_supertree.pdf** * This file is an illustration of
 the supertree obtained from the superficial suturing of the two
 phylogenetic datasets employed in this study * **Variable description of
 CSV files *XXX*\_PCA.csv** * Each file contains the type of bone in its
 filename (*i.e.* replace *XXX* with Coracoid, Femur\_outline, Humerus,
 Ilium, Ischium, Pubis, Scapula) * First column contains the list of each
 individual (which includes the bone type plus the species name or
 inventory number) * Columns starting from second through the last one
 contain the result of each component of the PCA analyses (*e.g.* Comp1,
 Comp2, Comp3, etc.) * **Variable description of FAD\_LAD\_global.csv** *
 First column contains the taxa list * Second column contains the first
 occurrence in m.y. * Third column contains the last occurrence in m.y. *
 **Convergence.R** which is the R script to run the updated Stayton
 distance-based convergence analysis * **Variable description of CSV files
 *XXX*\_pair.csv** * Each file contains the type of bone in its filename
 (*i.e.* replace *XXX* with Coracoid, Femur\_outline, Humerus, Ilium,
 Ischium, Pubis, Scapula) * The first column contains the name of the first
 taxon of the pair * The second column contains the name of the second
 taxon of the pair * Each line corresponds to one set or pair to be
 compared in the * Stayton\_results.zip contains all the Stayton
 distance-based convergence test (Ct metrics) results in CSV. Each CSV file
 corresponds to the Stayton analysis of one pair of crocodyliform for one
 bone which is detailed in the name of the file (*e.g.*
 *Stayton\_Coracoid\_Mecistops\_cataphractus\_Hyposaurus\_natator*
 corresponds to the coracoid bone for the pair *Mecistops cataphractus --
 Hyposaurus natator*): * **Variable description of CSV files** * Each line
 corresponds to a Ct metrics (*i.e.* Ct1, Ct2, Ct3, etc.) * First column
 contains the name of the Ct metrics (*i.e.* Ct1, Ct2, Ct3, etc.) * Second
 column contains the value of the Ct metrics * Third column contains the
 p-value associated with the Ct metrics * Landmark\_Phylomorpho.zip
 contains all the necessary FAD\_LAD and Bone\_convert data per bone (in
 CVS) to run the analyses from Code.R and Code\_LandmarkCombine\_updated.r.
 It contains: * **Jouve2020.nex** which is the nexus file of the
 phylogenetic data from S. Jouve and N. E. Jalil. *Paleocene resurrection
 of a crocodylomorph taxon: Biotic crises, climatic and sea level
 fluctuations*. Gondwana Research, 85:1–18, 2020a. ISSN 1342937X. doi:
 10.1016/j.gr.2020.03.010. * **Variable description of CSV files
 Bone\_convert\_*XXX*.csv** * Each file contains the type of bone in its
 filename (*i.e.* replace *XXX* with Coracoid, Femur\_outline, Humerus,
 Ilium, Ischium, Pubis, Scapula) * First column contains the list of taxa
 as it appears in the phylogenetic dataset * Second column contains the
 list of taxa with the filename corresponding to each 3D model * **Variable
 description of CSV files FAD\_LAD\_*XXX*.csv** * Each file contains the
 type of bone (*i.e.* replace *XXX* with Coracoid, Femur\_outline, Humerus,
 Ilium, Ischium, Pubis, Scapula) or set of bones (*i.e.* replace *XXX* with
 Thoracic, Pelvic, Total) in its filename * First column contains the taxa
 list * Second column contains the first occurrence in m.y. * Third column
 contains the last occurrence in m.y. ## Sharing/access Information 1.
 Phylogenetic data from S. Jouve and N. E. Jalil. *Paleocene resurrection
 of a crocodylomorph taxon: Biotic crises, climatic and sea level
 fluctuations*. Gondwana Research, 85:1–18, 2020a. ISSN 1342937X. doi:
 10.1016/j.gr.2020.03.010. 2. The original raw meshes (from laser or
 white-light scans) are available on Morphosource (Project ID: 000532738):
 3. Scripts and repaired 3D models are available on Dryad:
 https://doi.org/10.5061/dryad.qfttdz0p5 4. Scripts and repaired 3D models
 are also available on ORBi :
 [https://hdl.handle.net/2268/305703](https://hdl.handle.net/2268/305703)
 This dataset also contains the author preprint (embargo until 08-10-2024)
 ## Usage notes * R scripts require the free statistical software R; * 3D
 models are PLY and can be viewed with a variety of software * Landmark
 coordinates were originally taken with Checkpoint Stratovan