DOI: 10.5061/dryad.2280gb642
title: Data and code from: Complete metamorphosis promotes morphological and functional diversity in Caudata

description: Metamorphosis, a common and spectacular developmental process, involves
 major phenotypic changes often linked to environmental transitions.
 Understanding how these changes affect morphological evolution is crucial
 for examining metamorphosis's evolutionary impacts. In this study, we
 analysed the role of metamorphosis and life cycle variation on the
 morphological evolution of the mandible in Caudata (salamanders and
 newts), a clade that exhibits a great diversity of life cycles and
 ecologies. We focused on the mandible, a key component of the masticatory
 apparatus, to investigate how life cycle variation may influence the
 diversification of feeding mode. Using 3D geometric morphometrics on 317
 extant species of Caudata, we found that both life cycle and size
 influence mandible shape, with complex interactions between these factors.
 The morphology of the mandibular bones evolved more independently in
 species undergoing complete metamorphosis compared to those with partial
 metamorphosis, likely facilitating feeding diversification in terrestrial
 adults. On the other hand, high morphological integration in species
 undergoing partial metamorphosis could promote the rapid evolution of
 traits, resulting in the differentiation of more disparate morphologies,
 potentially aiding paedomorphic species in adapting to challenging
 environments. This study highlights the interplay between metamorphosis
 and the environment in shaping morphological evolution among species and
 provides new insights into the role of heterochrony in the morphological
 diversification of organisms.
description: # Data and code from: Complete metamorphosis promotes morphological and
 functional diversity in Caudata
 [https://doi.org/10.5061/dryad.2280gb642](https://doi.org/10.5061/dryad.2280gb642) ## Description of the data and file structure This repository contains all the data and code used in the manuscript entitled 'Complete metamorphosis promotes morphological and functional diversity in Caudata.' All code is written in the R language (R Core Development Team, 2022). If you use these data, please cite Louppe et al., 2025. ## **Data files** The data files are named **phylogeny_data, data_all, data_dent,** and **data_artang**. * **phylogeny_data** contains the time-calibrated phylogeny used in the study. * The three **data** files correspond to lists of matrices containing, for each species included in the phylogeny: * **Y**: The dataset landmarks, including all landmarks for **data_all**, those corresponding to the dentary for **data_dent**, and those corresponding to the prearticular-angular complex for **data_artang**. * **lc**: Life cycle categories. * **lc_fine**: Refined life cycle categories. * **habitat**: Habitat categories. * **habitat2**: Refined habitat categories. * **lc_habitat**: Categories integrating life cycle and habitat. * **csize**: Centroid size estimated from landmarks. * **family**: The family to which the species belongs. ## Code file The file **louppe_et_al_code** contains the script used to perform all the analyses in this study. The script is structured by analysis type and includes annotations describing each data manipulation and calculation step. For more details, refer to the **Methods** section of the publication. * **Data preparation**: Loading data. * **Fitting evolutionary models**: Fitting and assessment of multiple evolutionary models using functions from the **mvMORPH** package. * **Phylogenetic MANOVA and MANCOVA**: MANOVA/MANCOVA tests and effect size estimations using functions from the **mvMORPH** package. * **Test for allometry**: Testing allometry within each life cycle category using functions from the **mvMORPH** package. * **DFA**: Discriminant function analyses using functions from the **mvMORPH** package, with plots generated using the **ggplot2** package. * **Phylogenetic PCA**: Phylogenetic principal component analyses using functions from the **mvMORPH** package. * **Visualizing allometry**: Plotting allometric trajectories for each life cycle category using the **mvMORPH** and **ggplot2** packages. * **Disparity**: Shape disparity analyses using functions from the **dispRity** package, with plots generated using **ggplot2**. * **Rate of evolution**: Assessing rates of morphological evolution using functions from the **mvMORPH** package, with plots generated using **ggplot2**. * **Integration and modularity**: Phylogenetically informed integration and modularity analyses using functions from the **geomorph** package, with plots generated using **ggplot2**. * **Ancestral state reconstruction**: Ancestral state estimation using functions from the **phytools** package, parallelized runs using functions from the **foreach** and **doParallel** packages, and plots generated using **ggplot2**.