Data for: Phylogenetic structure of body shape in a diverse inland ichthyofauna
Data files
Jan 12, 2024 version files 485.46 KB
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3D_landmarks.zip
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family_skeletal.tre
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README.md
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Slicer_GPA_output.zip
Abstract
Body shape is a fundamental metric of animal diversity affecting critical behavioral and ecological dynamics and conservation status, yet previously available methods capture only a fraction of total body-shape variance. Here we use structure-from-motion (SFM) 3D photogrammetry to generate digital 3D models of adult fishes from the Lower Mississippi Basin, one of the most diverse temperate-zone freshwater faunas on Earth, and 3D geometric morphometrics to capture morphologically distinct shape variables, interpreting principal components as growth fields. The mean body shape in this fauna resembles plesiomorphic teleost fishes, and the major dimensions of body-shape disparity are similar to those of other fish faunas worldwide. Major patterns of body-shape disparity are structured by phylogeny, with nested clades occupying distinct portions of the morphospace, most of the morphospace occupied by multiple distinct clades, and one clade (Acanthomorpha) accounting for over half of the total body shape variance. In contrast to previous studies, variance in body depth (59.4%) structures overall body-shape disparity more than does length (31.1%), while width accounts for a non-trivial (9.5%) amount of the total body-shape disparity.
README: Data from: Phylogenetic structure of body shape in a diverse inland ichthyofauna
DOI: 10.5061/dryad.n2z34tn2t
We placed 11 homologous landmarks on 3D models representing the fish fauna of the Lower Mississippi River Basin to explore phylogenetic structure of body shape across an entire fauna.
This dataset contains raw 3D landmark data of 232 3D models of fishes, supplementary tables, Slicer GPA outputs, and R scripts to reproduce the analyses and figures of the morphospaces.
Description of the data and file structure
Landmark Data:
"3D_landmarks" - Folder containing raw (before Procrustes superimposition) landmark data exported from Slicer in .fcsv format. These files can be viewed using Microsoft Excel or your choice of text editor.
"Slicer_GPD_output" - Folder containing output files after processing the raw 3D landmark files in the SlicerMorph GPA module. The "analysis.log" file lists all specimens used and what files for R to reference when running the analysis to extract principal components (PCs), centeroids, mean shapes, etc. It is to be loaded into R and used with the "LA_Fishes_Master_Script.R" script file. All of the files in this folder can be opened with Microsoft Excel or your choice of text editor.
Contents:
-"analysis.log" - Log file from Slicer output. This is the file that is loaded into R to perform the analysis using the provided R script.
-"eigenvalues.csv" - This file reports eigenvalues for 33 principal components (PCs). These eigenvalues are unitless as they result from 3D landmark coordinates.
-"eigenvectors.csv" - Eigenvectors of each principal component (PC) are reported for all 11 landmarks in three dimensions (X,Y,Z). Eigenvectors have direction but no units.
-"MeanShape.csv" - Landmark coordinates in three dimensions (X,Y,Z) representing the calculated mean shape in the analysis as calculated by the Slicer GPA module.
-"OutputData.csv" - File containing procrustes distances, centeroid, and landmark coordinates in three dimensions (X,Y,Z) for each specimen used in the analysis (Sample_name). These data are unitless.
-"pcScores.csv" - File reporting PC scores (PC1, PC2, etc.) for each specimen used in the analysis (Sample_name). These data are unitless.
"family_skeletal.tre" - a tree file of all fish families from Rabosky et al. 2018. This file can be opened using the software FigTree or any other phylogenetic tree editing software and is meant to be loaded into R using the scripts provided.
Supplemental tables uploaded to Zenodo:
"ST1.xlsx" - Table of all specimens photographed to create 3D models used in the analysis. Specimens are organized by taxonomic order, family, and species, and includes total length (TL) in mm and museum catalog numbers.
"ST2.xlsx" - Table of PC loadings for all models used in the analysis generated from running a PCA of the landmark data using R as seen in the accompanying R script. Models are identified by a unique model name and the top 26 PC scores are reported as Comp1-Comp26. These data have no units.
Code/Software
Models were landmarked in the program Slicer.
All subsequent analyses were performed in the R statistical environment Version 2022.12.0+353.
R scripts to reproduce the analyses and figures are described as follows:
"LA_Fishes_Master_Script.R" - R code used to generate the figures and analysis presented in the manuscript.
Methods
3D models of fish specimens from the Lower Mississippi Basin were created using SFM 3D photogrammetry. The models were then landmarked in three dimensions using the free program Slicer. Landmark files for each model were exported from Slicer and are found in the "3D_landmarks" folder. The landmarks files were loaded back into Slicer and processed using the GPA module. The GPA module outputs were exported as the folder "Slicer_Output".
Usage notes
Landmark files in the "3D_landmarks" folder are in .fcsv format can be read by common text editors or Microsoft Excel. They can also be loaded into R.
"Slicer_Ouput" files can be opened using any text editor or Microsoft Excel. They are loaded into R using scripts found in the "LA_Fishes_Master_Script.R" file.
Supplementary tables ST1 and ST2 are best viewed using Microsoft Excel.
"family_skeletal.tre" - Tree topology from Rabosky et al. 2018 of all actinopterygian fish families to be loaded into R using the scripts provided. Can also be viewed in FigTree.