DOI: 10.5061/dryad.z08kprrqf
title: Macroevolutionary role reversals in the earliest radiation of bony fishes

description: 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.
description: # Macroevolutionary role reversals in the earliest radiation of bony
 fishes
 [https://doi.org/10.5061/dryad.z08kprrqf](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:** 1. 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 2. 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