Fig 1.
Main anatomical features of the temporal bone and petrous portion: a) human skull with the temporal bone highlighted, b) temporal bone from lateral view, c) temporal bone from internal view showing the petrous portion; d) internal detail of the petrous bone showing the location and position of the inner and middle ear.
The drawings were created by Sergio Monteiro Da Silva..
Fig 2.
µCT scans of a temporal bone showing the segmented inner ear or bony labyrinth (highlighted in magenta) in a) anterior, b) lateral, and c) postero-lateral views. In each image a-d, the two upper panels display 3D models of the temporal bone and the inner ear (the left one with texture, and the transparent right one showing the inner ear).
The three lower panels show 2D slices in the anatomical orthogonal planes indicated above: R(Red) = axial, G(Green) = sagittal, and Y(Yellow) = coronal. This Figure was created using 3D Slicer Preview Release 5.9.0 ([46]; https://www.slicer.org) and Inkscape..
Table 1.
Key variables for assessing ancient DNA authenticity, quality, and contamination.
Fig 3.
Comparison of aDNA preservation and contamination parameters in µCT-scanned (“True”; n = 13 for nuclear contamination; n = 50 otherwise) and not µCT-scanned (“False”; n = 18 for nuclear contamination; n = 43 otherwise) petrous samples:
(a) Endogenous content: percentage of unique reads mapping to the human reference genome; (b) Average read length mapping to the human reference genome; (c) Frequency of C → T transitions at the 1st base-pair of the 5’ end of the reads for half-UDG treated DNA libraries, and for (d) non-UDG treated DNA libraries; Contamination estimates (in %) based on (e) mitochondrial DNA (with ContamMix, f) and nuclear DNA (f, only for XY individuals). p-values are derived from a Wilcoxon rank-sum test conducted in R [60].
Table 2.
Description and operational values of µCT-scanning parameters applied in the present study.
Table 3.
Wilcoxon rank-sum test results comparing µCT-scanned and unscanned petrous bones across key molecular parameters. Sample sizes vary by metric: for all parameters except nuclear contamination, n = 50 (scanned) and n = 43 (non-scanned); for nuclear contamination (XY individuals only), n = 13 (scanned) and n = 18 (non-scanned). No statistically significant differences were detected for any parameter considered here (p > 0.05; see also Fig 3).
Fig 4.
Workflow proposed for a sustainable and interdisciplinary approach to human evolution studies.