Macroevolutionary role reversals in the earliest radiation of bony fishes
Data files
Sep 01, 2025 version files 139.33 MB
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R_code.zip
139.31 MB
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README.md
2.78 KB
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Supplemental_Appendix_1.xlsx
21.90 KB
Abstract
The evolution of jaws is hypothesized to have fueled radiations among vertebrates, contributing to their overwhelming success in the present day. Past work shows rapid early expansion of diversity in jaw structure in many lineages; however, the evolutionary dynamics underlying this pattern are unclear and hindered by the lack of a robust comparative framework. Here, using a macroevolutionary approach, we explore the diversification of lower jaws in early bony fishes, a major contributor to this initial radiation. Using newly generated three-dimensional mandibular shape data from 86 species, we find evidence of adaptive radiation in jaws during the earliest interval of bony fish evolutionary history (423-359 Ma.). These patterns are principally driven by early lungfishes and coelacanths, which display high rates of jaw diversification, rapid shifts into novel functional regions of trait space, as well as substantial innovation in jaw morphology and feeding ecology, standing in contrast to their "living fossil" descendants of today. Conversely, ray-finned fishes and tetrapodomorphs, morphologically diverse groups in the present day, show little indication of their future success, possessing slow rates of jaw evolution and low functional diversity. This profound inversion of patterns in modern taxa highlights the significance of paleontological data in understanding drivers of evolutionary diversification and the limitations of approaches using only living species. Overall, our findings provide insight into the evolutionary dynamics associated with the evolution of jaws and provides context for the role of jaws in vertebrate success.
https://doi.org/10.5061/dryad.z08kprrqf
1. Project Description:
Evolutionary analysis of jaw shape in early Devonian bony fishes. This supplemental dataset contains supplemental Appendices 1 and a zipped folder of all R code and output needed to run the analysis within
2. Contents:
Appendix 1: Supplemental_Appendix_1.xlsx
Description: Spreadsheet file containing a list of species CT scanned, including institution, collection code, specimen number, where the model is archived, and stratigraphy information.
Appendix 2: R_code.zip
Description: Zipped folder containing all files and code needed to reproduce results from all R analyses
Folder 1 Name: BayesTraits
Folder 1 Description: Output from BayesTraits analyses. There are two subfolders (PC_analysis; pPC_analysis), each subfolder contains the output .txt files from BayesTraits analysis on PC data and pPC data, respectively.
Folder 2 Name: Coords
Folder 2 Description: There are two files here (all_landmarks_array.RDS) and (data_shape_array_jaws.RDS). They contain all the landmark coordinates for the 86 species used in the analysis and the jaw shape array, respectively.
Folder 3 Name: Landmarks
Folder 3 Description: There are 33 subfolders within this Landmarks folder. Each folder is named according to the species it represents. Within each folder are 6 files, all ending in .json. These are the 5 curve files and 1 landmark file created in 3D Slicer.
File 1 Name: 00_Devonian_Jaws_Final_Code_for_Dryad.R
File 1 Description: The R source code needed to run all analyses in the manuscript.
File 2 Name: curveslide.csv
File 2 Description: File containing the curve sliders for landmark analysis
File 3 Name: Data_for_PCA_plots_86spp.csv
File 3 Description: Data table for each of the 86 species used in this study. Columns include information for specimen Class, Clade, color scheme for plotting, Age, Period, jaw centroid sizes, jaw lengths, and tip ages.
File 4 Name: Devonian_Jaws_Results_May_23_2025.RData
File 4 Description: This is an R Data file containing all the saved results from all R analyses
File 5 Name: MrBayes_nodata_v3.con.tre
File 5 Description: This is the consensus tree from the MrBayes analysis
3. Usage:
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Open the "00_Devonian_Jaws_Final_Code_for_Dryad.R" into R. It is well-annotated. Simply follow all steps in this file if you want to run the analyses yourself
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Load "Devonian_Jaws_Results_May_23_2025.RData" into R. This will bring up all saved results for all analyses if you don't want to run the analyses yourself.
Missing data code: NA
4.Code/Software:
Analyses were run in R version 4.2.3