Population history and positive assortative mating directs gene flow in such a way that biological
differences are recognized among groups. In turn, forensic anthropologists quantify biological
differences to estimate ancestry. Some anthropologists argue that highly admixed population groups,
such as South African coloureds, cannot achieve acceptable accuracies because within group variance is
too large. Whereas ancestry estimation in South Africa has been limited to craniometric data from South
African blacks and whites, the current study integrates craniometric and geometric morphometric data
from the three largest South African groups.
Crania from 377 South African individuals (black = 158, white = 112, and coloured = 107) comprised
the sample. Standard measurements were collected and the coordinate data were subjected to
Generalized Procrustes Analysis (GPA), which resulted in size-free shape variables (ProCoords). A
principal component analysis was used to combine the shape variation captured in the ProCoords
(ProCoords PC). Linear discriminant analysis (LDA), using equal priors, stepwise variable selection and
leave-one-out cross-validation, was conducted on the ProCoords, the ProCoords PCs, and the traditional
The LDA using 18 stepwise selected ProCoords resulted in the highest cross-validated accuracy (89%).
Utilization of geometric morphometric data emphasized that the relative location of cranial landmarks
was more discriminating than simple linear distances. Regardless of high levels of genetic admixture,
South African coloureds are a homogeneous group and morphologically distinct from other
contemporaneous South African populations. Furthermore, the present study demonstrated a
correspondence between peer-reported race and morphological differences in the crania of black,
white, and coloured South Africans.