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Category: Data

Description: These data are associated with the manuscript "Convergent evolution in Afrotheria and non-afrotherians demonstrates high evolvability of the mammalian inner ear". They correspond to a 3D geometric morphometric analysis of the shape of the bony labyrinth (the osseous surrounding of the inner ear) in 40 extant mammal species: 20 Afrotheria, compared to non-Afrotheria (18 Placentalia, 1 Marsupialia, 1 Monotremata). 6 files are provided in the OSF repository (data sets): * The sample composition (CSV file) is a data sheet with information about the 40 specimens, their taxonomy and the CT-scan resolutions; * The README file (CSV file) is a data sheet with a description of the content of the sample composition file; * The phylogeny (TXT file) is an ultrametric tree written in Nexus format; * The contextual data (CSV file) is a data sheet with the 12 contextual variables including body mass, as well as the "habitat groups" used only for visualization in the scatter pots of PCA or PLS scores. For the key to the variable codes in the contextual data, see Table 2 in the main manuscript; * The 3D surface models (PLY files) correspond to the bony labyrinth extracted from microCT-scans for one side of the skull of the 40 specimens; * The raw landmarks (CSV file) is a data sheet with the raw 3D landmark coordinates taken on the bony labyrinth of each species. Landmark coordinates are in the order of the landmarks in Table 3 in the main manuscript: first the 13 anatomical landmarks, then the 111 semilandmarks; * The slid landmarks (CSV file) is a data sheet with the 3D landmark coordinates after the step of sliding the semilandmarks but before the GPA (the ordering of the landmarks is the same as in the raw landmark file). The latter can be used for a GPA without sliding. Specimens are ordered depending on their taxonomy in the sample composition file, whereas they are ordered alphabetically (Linnean names) in the raw landmarks, slid landmarks and contextual data files. 7 other files are provided in a GitHub folder: * README.md: a Markdown file describing the content of the R scripts and the data sets required for the analyses; * 00_Definitions.R: R script (required for the other R scripts) to define the landmark parameters, prepare the contextual data, and create the function `plotLaby` for 3D visualization of shape patterns * 01_GPA.R: R script to slide semilandmarks, perform the GPA, find outliers, and perform some visualizations * 02_ProcD.R: R script to compute pairwise Procrustes distances and related cross-validations * 03_PCA.R: R script to perform a PCA of the Procrustes shape coordinates * 04_PLS.R: R script to perform the 2B-PLS between the landmark coordinates and the 12 contextual variables, related cross-validations, compute the phylogenetic signal in the PLS scores, and do a phylogenetic PLS * 05_WI.R: R script to compute the Wheatsheaf index (Arbuckle et al. 2014 Meth. Ecol. Evol.)