Data from: Limited convergence in the postcranium of aquatic crocodylomorpha
Data files
Nov 14, 2023 version files 1.08 GB
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Code_LandmarkCombine_updated.r
30.86 KB
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Code.R
42.88 KB
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Convergence_Pairs.zip
45.93 KB
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Convergence.R
7.34 KB
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Landmark_Phylomorpho.zip
39.42 KB
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Models.7z
770.66 MB
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Phenogram.zip
5.73 KB
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README.md
11.52 KB
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Stayton_results.zip
17.18 KB
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ThalattoONLY.7z
313.20 MB
Abstract
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 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.
- Each bone XXX subfolder contains:
- 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
- Description of FigSX_supertree.pdf
- 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
- Variable description of CSV files
- 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
- 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.
- The original raw meshes (from laser or white-light scans) are available on Morphosource (Project ID: 000532738):
- Scripts and repaired 3D models are available on Dryad: https://doi.org/10.5061/dryad.qfttdz0p5
- Scripts and repaired 3D models are also available on ORBi : 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
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
- 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