Ancestry estimation in South Africa using craniometrics and geometric morphometrics

Abstract

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 2 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 leaveone-out cross-validation, was conducted on the ProCoords, the ProCoords PCs, and the traditional craniometric data.The LDA using 18 stepwise selected ProCoords resulted in the highest crossvalidated 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.

Population differences in the postcrania of modern South Africans and the implications for ancestry estimation

“…South Africa provides a testament to how geographical and social factors can influence population variation. The wide range of morphological variation among groups in South Africa is the cumulative result of varying geographic origins, unique population histories and structure, positive assortative mating and social and/or political barriers [4][5][6][7].…”

“…Parental populations are inclusive of (1) indigenous Khoesan, (2) descendants of slaves brought from countries such as Malaysia, Indonesia and 4 India, (3) Europeans and (4) Bantu-speaking groups [14,[17][18][19]. The different group histories shaped the unique and heterogeneous basis of modern variation among South Africans [6].…”

“…Numerous studies identify the cranium as the most accurate element to estimate ancestry; specifically, inclusion of midfacial variables in metric analyses can increase the accuracy of classification models [6,[20][21][22]. Using standard linear cranio-metric variables the South African literature reports accuracies ranging from 98% between black and white South Africans [20] to 84% accuracy with a three group classification among black, white and coloured groups [23].…”

“…Decades of positive assortative mating and segregation limited gene flow among the groups and enabled morphological differences to be maintained among modern South Africans [6]. Higher levels of within-group variation was noted among black and coloured South Africans, ultimately resulting in substantial group overlap.…”

Composition of the Kirsten Skeletal Collection at Stellenbosch University

“…Current research using human skeletal collections includes developing new techniques to test and standardise regional-specific data regarding osteometric measurements and physical observations. [1][2][3][4][5] These reference points provide practical information for the estimation of biological profiles of unknown skeletons 6 in both forensic anthropology and bioarchaeology, including estimation of age, sex and stature. Detailed descriptions of skeletal remains of known populations are used to confirm or contradict archaeological and social theories for past and present communities.…”