Adaptive radiation of pelagiarian fishes at the K/Pg boundary led to rapid diversification of mandible morphology
Data files
Nov 21, 2025 version files 272.76 MB
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morphometrics.zip
272.75 MB
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README.md
6.68 KB
Abstract
Mandibles represent a key evolutionary innovation that have enabled jawed vertebrates to adapt and diversify in response to a range of food sources, and changes in mandible shape are often linked with adaptive radiations into new ecological niches. Using a phylogenetic comparative approach, we explore the phenotypic disparity and mechanical properties of the lower jaw in Pelagiaria, a morphologically diverse but relatively small clade of open-ocean fishes which arose near the Cretaceous/Paleogene (K/Pg) mass extinction event. Using three-dimensional (3D) geometric morphometrics, we find that the high phenotypic disparity of the pelagiarian mandible was established very early in their evolutionary history, and high levels of disparity have been maintained over tens of millions of years; this is consistent with the hypothesis that Pelagiaria represents an ancient adaptive radiation. We test the correlation of mandible shape with potential drivers of shape evolution, and find that mandible shape is correlated with habitat depth and tooth type, but not with body elongation or diet. Moreover, mandible shape is significantly correlated with mechanical advantage (MA), with closing MA being most strongly correlated. Pelagiarian jaw shapes fall broadly into six morphotypes, of which two show significantly higher closing MA than other groups, despite differing substantially in shape. Our results demonstrate both the mechanical and morphological diversity of the pelagiarian mandible and support the hypothesis that Pelagiaria underwent repaid morphological diversification early in their evolution, likely due to adaptive radiation.
Dataset DOI: 10.5061/dryad.n2z34tnbm
Description of the data and file structure
This repository contains all data, scripts, and supplementary figures from "Adaptive radiation of pelagiarian fishes at the K/Pg boundary led to rapid diversification of mandible morphology."
Code/software
All code is written for R (v. 2024.12.1+563), with required packages labelled at the start of each script. Packages should be installed prior to running scripts.
The scripts for replicating this study should be run in order.
Morphometrics
1.1 Contents
morphometrics.zip: Run through scripts in 'scripts' folder in numbered order.
morphometrics
┣ input_data
┃ ┣ mandible_resampling_template.csv
┃ ┣ mandible_specimen_data.csv
┃ ┗ mandible_tree.nex
┣ output_data
┃ ┣ PCA.3D.rda
┃ ┣ slidedlms.mandible.rda
┃ ┗ Y.gpa.rda
┣ ply_ASCII
┣ pts
┣ scripts
┗ ┣ 1.functions.R
┣ 2.curve_resampling_sliding.R
┣ 3.basic_shape_analysis.R
┣ 4.ecology.R
┣ 5.disparity_through_time.R
┗ 6.cluster_analysis.R
1.2 Description of files and variables
1.2.1 input_data
File: skull_resampling_template.csv
Description: Table containing template for standardised resampling of skull semilandmark curves, used in 2.curve_resampling_mandible.R script. Information includes start point, end point, and the number of curves required for each curve. Only lm1,lm2, and ptswanted columns are necessary for the curve resampling script.
Variables
- Curves: Curve identifier number
- lm1: Start point of curve (landmark number)
- lm2: End point of curve (landmark number)
- ptswanted: Number of points needed for resampling
- start: Landmark number of start of curve (after resampling, excluding lm1)
- end: Landmark number of end of curve (after resampling, excluding lm2)
File: mandible_specimen_data.csv
Description: Contains information for all 137 species included in the study. Variables are listed below; see methods for definitions.
Variables
- species: Name of species, with space
- species.2: Name of species, with underscore
- genera: Genera of species
- family: Family of species
- tooth: Tooth classification of each species (edentulate, microdont, macrodont, villiform)
- diet: Diet classification of each species (fish, jellyfish, zooplankton)
- ratio: Ratio of body length to body depth
- depth: Depth category of each species (shallow, intermediate, deep)
- MA_open: Mechanical advantage of jaw opening (MAopenA)
- MA_close: Mechanical advantage of jaw closing (MAclose)
- MA_open_b: Mechanical advantage of jaw opening (MAopenB)
File: mandible_tree.nex
Description: Full-time-scaled phylogeny in Nexus format for 137 species included in the study.
Folder: ply_ASCII
Description: Contains three-dimensional (3D) mandible surface meshes for all 137 species included in the study, in ASCII .ply format and used in 2.curve_resampling_mandible.R script. Meshes are scaled in mm and can be opened and viewed in any 3D viewing software that supports .ply format.
Folder: pts
Description: Individual mandible landmark files for all 137 species included in the study and used in 2.curve_resampling_mandible.R. Landmark files are in pts format and each contains 8 anatomical (Bookstein Type I and II) landmarks and 10 semilandmark curves. Each row represents a single landmark and contains three columns of X, Y, and Z spatial coordinates. Refer to the Supplementary File for details of each landmark.
1.2.2 output_data
This folder contains output files generated in the morphometrics section.
File: PCA.3D.rda
Description: R file containing PCA eigenvalues for mandible landmarks.
File: slidedlms.mandible.rda
Description: R file containing landmarks and resampled and slid semilandmark curves for all specimens, created in the 2.curve_resampling_sliding.R script.
File: Y.gpa.rda
Description: R file containing Procrustes-aligned landmark coordinates for all specimens.
2 Instructions for running morphometric analyses.
2.1 Data
morphometrics/input_data/ contains input data needed to run morphometric analyses, including species data for all specimens (mandible_specimen_data.csv), semilandmark curve resampling template (mandible_resampling_template.csv), and the full, timescaled phylogeny for the dataset (mandible_tree.nex).
morphometrics/output_data/ contains the output from the morphometric analyses, including processed landmarks for all specimens, slidedlms.mandible.rda output from 2.curve_resampling_mandible.R, Procrustes alignments Y.gpa.rda, and principal component analyses PCA.3D.rda for all specimens.
morphometrics/ply_ASCII/ contains meshes for all mandibles used in the analysis, in ply ASCII format.
morphometrics/pts/ contains landmark data for all specimens.
2.2 Code
morphometrics/scripts/ contains all scripts required to run morphometric analyses on the dataset, which should be run in order. All required packages are listed in the scripts and should be installed prior to running the scripts. 1.functions.R contains functions required to resample and slide semilandmarks once imported in 2.curve_resampling_sliding.R and should be run first in its entirety. The script 2.curve_resampling_sliding.R imports landmark data from morphometrics/pts/ resamples the semilandmark curves to standard numbers of landmarks based on the relevant mandible_resampling_template.csv file. The scripts include the process for estimating missing landmarks, sliding the resampled semilandmark curves to minimise bending energy, and exporting the resultant landmark files as a single R script. 3.basic_shape_analysis.R imports the mandible landmarks from step 2, and performs a generalised Procrustes alignment followed by a principal component analysis on the Procrustes-aligned landmarks. 4.ecology.R performs MANOVAs on Procrustes-aligned shape data against ecological data included in mandible_specimen_data.csv, accounting for phylogeny. 5.disparity_through_time.R performs a disparity through time analysis on mandible shape data, plots the results of the analysis, and performs a rank envelope test on the results. 6.cluster_analysis.R calculates the optimum number of clusters in morphospace, and calculates, plots, and statistically compares the mean mechanical advantage for each cluster.