DOI: 10.5061/dryad.n2z34tn2t
title: Data for: Phylogenetic structure of body shape in a diverse inland ichthyofauna

description: 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.
description: 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".
  
description: 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.
description: # 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.