Data and code from: Complete metamorphosis promotes morphological and functional diversity in Caudata
Data files
Mar 28, 2025 version files 1.05 MB
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data_and_code.zip
1.05 MB
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README.md
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Abstract
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.
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.