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Supporting data for Evolution and development of the pseudosuchian skull table sutures and their impact on the cranial topology

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posted on 2023-04-03, 01:32 authored by Hiu Wai LeeHiu Wai Lee

  

Files are separate into two folders.

"Raw Data" is for the raw data used to run the analysis. 

"Thesis" is for the main text, figures, tables, and appendices and the raw images used to create the figures in the main text in the thesis. 

For CT scans and surface images of crocodilians, please ask Dr. Arkhat Abzhanov of Imperial College London, UK and Natural History Museum, UK and Dr. Zachary Morris of Yale University for permission to use them.

Raw Data Folder

Chapter 1 folder

Chapter 1 folder contains the following items: 

“Example of NIMS.rmd” is the R script used for each matrix in “Matrices of pseudosuchians and non-archosaurian archosauriforms” folder to generate the parcellation score. 

“All specimens Pseudosuchian Project.rmd”, “Adult Pseudosuchian Project.rmd”, and “extinct pseudosuchians only.rmd” are the R scripts that import the matrices from “Matrices of pseudosuchians and non-archosaurian archosauriforms” and parcellation scores, run the analyses, and export outputs in the “Output files” folder for all specimens, a subset of adult specimens, and a subset for extinct specimens. 

“Centrality for pseudosuchians.rmd” is the R script used to import the matrices, run the analysis for centrality, and generated the “11.23 Centrality.xlsx” that would be used for Chapter 2. 

“Pseudosuchian Dataset Representative networks for each clade based on median of PC1.rmd” is the R code that imports the matrices to generate SVG and PNG figures of the networks used for the main figure in the thesis. 

“Phylogenetic tree with two Erpetosuchus position.R” is the R code that generates the phylogenetic tree used for the main figure in the thesis. 

Chapter 2 folder

Chapter 2 folder contains the following items: 

“Example of NIMS.rmd” is the R script used for each matrix to generate the parcellation score. 

“2021.10.11 adult crocs + adult birds +adult Dino remove Dilophosaurus.rmd” is the R scripts that import the matrices from “Matrices adult pseudosuchians and avemetatarsalians”, information about the adult birds from “List of taxa with adult birds.xlsx” and parcellation scores, run the analyses, and export outputs in the “Output files” folder for all adult specimens. 

“Centrality for adults.rmd” is the R script used to import the matrices, run the analysis for centrality, and generated the “11.23 Centrality of adult birds.xlsx” that would be used for Chapter 2. The same code is also used to generate “11.23 Centrality for juvenile birds.xlsx” by changing the name of the matrices in the code directly.

“biplot of clade by period.R” is the R code that imports the matrices to generate the PNG files in the “temporal graphs” folder, which are used for the main figure in the thesis and the “temporal graphs.gif” used in my presentation. 

“Fig 3A paleognath, galloanswerae, and Other Neoganthae.R” and “Figure3A Tree.R” are the R code that generate the phylogenetic trees “Fig3A. Calibrated phylogeny of Avemetatarsalia.svg” amd “Fig3A2. Calibrated phylogeny of Avemetatarsalia.svg” used for the main figure in the thesis and manuscript. 

Chapter 3 folder

For Chapter 3 folder, the files are separated based on what analyses they are for. 

"4 Landmarks for orbits" contains 

"Landmarks": the orbital landmarks retrieved from Morris et al. (2021); 

"Zach orbit.rmd" is the R script to retrieve the orbit landmarks from the original files from Morris et al. (2021), run the analysis, and generate the output files; 

"Zach Landmark Taxa.csv" facilitates the R script by naming the specimens. 

"Output" contains the output files generated from the R script. 

"Frontoparietal suture" contains

"Landmarks" and "Adult landmarks": landmarks that were used to outline the shape of the frontoparietal sutures in all specimens and in a subset of adult specimens; 

"2022.11.28 PSD.rmd" and 

"2022.11.28 PSD and morphospace for Adult Specimens.rmd" are the R scripts from placing landmarks to running the analyses and generating the output files from all specimens and in a subset of adult specimens; 

“Nonparametric tests on PSD values.rmd’ is the R script to run nonparametric tests on PSD values with and without outliers using the “PSD_array and Csize.csv” and “PSD no Bover no C.nova.csv” from Output/All specimens folder; 

"taxa.csv" facilitates the R script by naming the specimens; 

"Curves.txt", "Curves1.txt", and "Landmarks.txt" facilitates the R script by naming the semilandmark curves and landmarks used; 

"Output" contains all the output files generated from the R script and is separated into "All specimens" and "Adults only" to distinguish the output files from all specimens and in a subset of adult specimens; and

"Test for using 720 semilandmarks" contains the outputs when the analysis is run using 720 semilandmarks. 

“Geometric morphometrics for developing sutural fronts of medial frontal and parietal” contains 

“GM analyses for left parietal.rmd”, “GM analyses for right parietal.rmd”

“GM for Left Frontal.rmd”, and “GM for Right Frontal.rmd” are the R scripts used to produce the semi-landmarks for the medial sutural fronts of the left and right parietal and frontal, run the analyses, and generated the output files;

“Semilandmarks” separate the semilandmark files into folders that match with their R scripts; 

“Output” separate the output files into folders that are generated by their respective R scripts

“Percentage sutural closure of interfrontal and interparietal” contains 

“Interfrontal and interparietal percentage fusion.csv”: raw percentage fusion recorded in each specimen; and,

“Sutural closure of interfrontal and interparietal sutures.twb”: the Tableau workbook used to generate Supplementary Figures C. 10 and C.11. 

Chapter 4 folder

Chapter 4 folder contains the “Histology photos” and the “Immunofluorescence images”. 

“Histology photos” has all the photos with scalebar, photos without scalebar (in a subfolder called “no scalebar”), and photos of the medial portion of the frontal or parietal bone “Medial portion of the frontal or parietal bone”. 

For all the photos in “Histology photos”, the first two letters indicated the staining (“AB” for alcian blue, “HE” for haematoxylin and eosin, “MT” for Masson’s Trichrome), the third and fourth letters indicate the slides used, the number after GgE (which stands for “Gallus gallus Embryonic”) is the embryonic stage, and the letter indicates the specimen used. Comments of the location of the photos are sometimes added in the name after the embryonic stage and specimen used. 

“Immunofluorescence images” has all the immunofluorescence images. Folders are named by developmental stage (in embryonic days) and the specimen. Each folder is further divided into “Frontal” or “Parietal” with subfolders named after the slide number and the primary antibody used. Then, in each folder are the .jpg files named by the magnification used and either the DAPI or primary body used. The .jpg_meta.xml files are generated from the imaging softwares and contain information about the imaging software. “Output” in these folders convert the black-and-white .jpg into .tif by using the “Convert bw images to colored.ijm” macro in ImageJ. “Scalebar” is a folder for the scalebar images of 10X and 20X magnification.   

Thesis 

Folder: Chapter 1

Short description: Main figures from Chapter 1 and Supplementary Tables and Figures for Appendix A. The files are listed in Appendix A Supplementary Materials for Chapter 1.docx. 

Folder: Chapter 2

Short description: Main figures from Chapter 2 and Supplementary Tables, and Figures for Appendix B. The files are listed in Appendix B Supplementary Materials for Chapter 2.docx. 

Folder: Chapter 3

Short description: Main figures from Chapter 3 and Supplementary Tables, Figures, and Information for Appendix C. The files are listed in Appendix C Supplementary Materials for Chapter 3.docx. 

Folder: Chapter 4

Short description: Figures from Chapter 4 and Supplementary Figures, and Information for Appendix D. The files are listed in Appendix D Supplementary Materials for Chapter 4.docx. 

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