DOI: 10.5061/dryad.000000094
title: Data from: A shared pattern of midfacial bone modelling in hominids suggests deep evolutionary roots for human facial morphogenesis

description: Midfacial morphology varies between hominoids, in particular between great
 apes and humans for which the face is small and retracted. The underlying
 developmental processes for these morphological differences are still
 largely unknown. Here we investigate the cellular mechanism of maxillary
 development (bone modelling), and how potential changes in this process
 may have shaped facial evolution. We analysed cross-sectional
 developmental series of gibbons, orangutans, gorillas, chimpanzees and
 present-day humans (N=183). Individuals were organized into five age
 groups according to their dental development. To visualize each species’
 bone modelling pattern and corresponding morphology during ontogeny, maps
 based on microscopic data were mapped onto species-specific age group
 average shapes obtained using geometric morphometrics. The amount of bone
 resorption was quantified and compared between species. Great apes share a
 highly similar bone modelling pattern, whereas gibbons have a distinctive
 resorption pattern. This suggests a change in cellular activity on the
 hominid branch. Humans possess most of the great ape pattern, but bone
 resorption is high in the canine area from birth on, suggesting a key role
 of canine reduction in facial evolution. We also observed that humans have
 high levels of bone resorption during childhood, a feature not shared with
 other apes.
description: Microscopic data on bone modeling patterns are collected from the
 maxillary bones of each species. Geometric morphometric techniques are
 used to obtain species-specific average shapes for each age group. Maps
 based on microscopic data are overlaid onto the species-specific average
 shapes to visualize bone modeling patterns and corresponding morphological
 changes during ontogeny. The amount of bone resorption is quantified and
 compared between species.
description: # A shared pattern of midfacial bone modelling in hominids suggests deep
 evolutionary roots for human facial morphogenesis
 [https://doi.org/10.5061/dryad.000000094](https://doi.org/10.5061/dryad.000000094) ## Description of the data and file structure The data made available for this study consist of the following: * The database containing information on each individual (reference number, collection, age group (AG), sex, and analyses performed (microscopic analysis (BM) and/or geometric morphometric (GM) analysis) * ***Database_Schuhetal.xlsx*** * Species: name of the species * REF: reference number * Collection: place where the material is stored * AG: age group (1 = newborns; 2 = deciduous dentition developing; 3 = M1 in occlusion; 4 = M2 in occlusion; 5 = M3 in occlusion) * Sex: M = male, F = female, Unk = unknown * CT or Surface scan used for an individual * Taken for microscopic analysis (BM): whether the individual was taken for the BM analysis or not depending on surface preservation * Taken for GM analysis (GM): whether the individual was included in the GM analysis or not (sometimes scans could not be used) * The matrices necessary ton run both the PC analysis on shape and bone modeling data and size (txt.files): * ***Labels.txt***** and *Labels_BM.txt*** * Name: ref number of the individual * Species * Group: age group * ***Mat_GPA.txt*** * Matrix of Procrustes distances * ***Mat_BM.txt*** * ***Mean.txt*** * Grand Mean of the sample (needed to compute the warps, see R code) * ***Size.txt*** * Matrix of centroid sizes * ***MinText_PCX.txt*** * Example of how to organize the file for the texture at each PC's extreme * The mean shapes of age groups 1,3 and 5 (or 2 if 1 is missing) and species (.ply) to compute the heatmaps * ***File "Mean shapes"** * * Example for age group 1 chimpanzee: ***Warp_AG1_Ch.ply*** * The txt files to compute the mean maps (see R code for when and how to use them) * ***Data_All_BM.txt, Ex_Mean_AG1_Pongo.txt*** * The txt files to compute the mean BM maps * ***Labels_BM.txt*** * Name: ref number of the individual * Species * Group: age group * ***Data_All_BM.txt*** * The txt file containing all individual maps (with percentages of bone resorption for each map * ***Ex_Mean_AG1_Pongo.txt*** * Example of how the txt file should be structured for the mean * The txt file to compute the boxplot * ***DF_BR.txt*** * Name: ref number of the individual * Species * Value: percentage of bone resorption * AG: age group * The R code to perform all these above steps (PCA analyses, heatmaps, and statistics) ## Code/Software The R (version 4.2.3.) script given available consists of codes on how to run a PCA on the shape and bone modeling data (figures 1 and 3), how to compute the extreme shapes/textures on each axis (figures 1 and 3), how to create the heatmaps (figure 2), how to create the mean bone modeling maps (figure 4), how to create the boxplot for figure 5, and how to run some statistics on the data.