DOI: 10.5061/dryad.n2z34tnbm
title: Adaptive radiation of pelagiarian fishes at the K/Pg boundary led to rapid diversification of mandible morphology

description: 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.
description: # Adaptive radiation of pelagiarian fishes at the K/Pg boundary led to
 rapid diversification of mandible morphology Dataset DOI:
 [10.5061/dryad.n2z34tnbm](https://doi.org/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
 (MA~openA~) * **MA_close:** Mechanical advantage of jaw closing
 (MA~close~) * **MA_open_b:** Mechanical advantage of jaw opening
 (MA~openB~) **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.