Data from: A shared pattern of midfacial bone modelling in hominids suggests deep evolutionary roots for human facial morphogenesis
Data files
Mar 26, 2024 version files 696.48 MB
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Data_All_BM.txt
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Database_Schuhetal.xlsx
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DF_BR.txt
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Ex_Mean_AG1_Pongo.txt
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Labels_BM.txt
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Labels.txt
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Mat_BM.txt
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Mat_GPA.txt
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Mean.txt
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MinText_PCX.txt
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README.md
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Schuh_et_al_Rcode.r
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Size.txt
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Warp_AG1_Ch.ply
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Warp_AG1_HS.ply
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Warp_AG1_Pong.ply
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Warp_AG2_Gib.ply
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Warp_AG2_Gor.ply
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Warp_AG3_Ch.ply
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Warp_AG3_Gib.ply
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Warp_AG3_Gor.ply
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Warp_AG3_HS.ply
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Warp_AG3_Pong.ply
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Warp_AG5_Ch.ply
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Warp_AG5_Gib.ply
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Warp_AG5_Gor.ply
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Warp_AG5_HS.ply
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Warp_AG5_Pong.ply
Abstract
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.
README: A shared pattern of midfacial bone modelling in hominids suggests deep evolutionary roots for human facial morphogenesis
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)
- Database_Schuhetal.xlsx
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
- Labels.txt** and Labels_BM.txt**
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
- **File "Mean shapes"* *
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
- Labels_BM.txt
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
- DF_BR.txt
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.
Methods
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.