Ancestry estimation in South Africa using craniometrics and geometric morphometrics

Cranial fluctuating asymmetry and its relationship with non-specific physiological stress indicators in a contemporary South African cadaveric skeletal sample

OBJECTIVES

Biological anthropologists frequently explore skeletal asymmetry, together with population health and disease. Given the conflicting findings in existing literature, this study aimed to clarify whether an association exists in a South African sample.

MATERIALS

Dry bone and cranial micro-focus X-ray Computed Tomography (micro-XCT) scans of 115 South African individuals were assessed.

METHODS

Fluctuating asymmetry (FA) indices were calculated from interlandmark distances, and the frequency of four types of non-specific signs of physiological stress were documented to explore the relationship between FA and disease.

RESULTS

Black South Africans did not exhibit a high FA index; however, they had the highest prevalence of non-specific signs of physiological stress. However, no significant correlations were detected between FA indices and pathological lesions.

CONCLUSION

No correlation was observed between FA and populations from different socio-economic backgrounds. However, individuals of lower socio-economic status (SES) demonstrated a greater prevalence of non-specific signs of physiological stress.

SIGNIFICANCE

This research suggests that skeletal indicators of stress may be a suitable biological marker for assessing differences in SES among population groups, while indicating that levels of cranial FA is an inadequate biological marker.

LIMITATIONS

Possible limitations may include measurement error, and the lack of information on the life history and medical records of individuals in this sample.

SUGGESTIONS FOR FURTHER RESEARCH

Future research should include a larger sample with more South African groups, and should evaluate the potential association among age, FA, and expression of skeletal markers of disease.

Exploring cranial macromorphoscopic variation and classification accuracy in a South African sample

To date South African forensic anthropologists are only able to successfully apply a metric approach to estimate population affinity when constructing a biological profile from skeletal remains. While a non-metric, or macromorphoscopic approach exists, limited research has been conducted to explore its use in a South African population. This study aimed to explore 17 cranial macromorphoscopic traits to develop improved methodology for the estimation of population affinity among black, white and coloured South Africans and for the method to be compliant with standards of best practice. The trait frequency distributions revealed substantial group variation and overlap, and not a single trait can be considered characteristic of any one population group. Kruskal-Wallis and Dunn's tests demonstrated significant population differences for 13 of the 17 traits. Random forest modelling was used to develop classification models to assess the reliability and accuracy of the traits in identifying population affinity. Overall, the model including all traits obtained a classification accuracy of 79% when assessing population affinity, which is comparable to current craniometric methods. The variable importance indicates that all the traits contributed some information to the model, with the inferior nasal margin, nasal bone contour, and nasal aperture shape ranked the most useful for classification. Thus, this study validates the use of macromorphoscopic traits in a South African sample, and the population-specific data from this study can potentially be incorporated into forensic casework and skeletal analyses in South Africa to improve population affinity estimates.

A consolidated summary of South African human skeletal repositories

AIM

Human skeletal repositories are crucial resources for research and education in human biology, variation, anatomy, biocultural frameworks, forensic/medico-legal casework, heritage and understanding the past. In this review paper, we assess the composition of human skeletal repositories in South Africa, along with the ethical and legal frameworks that safeguard their curation.

METHODS

The data and information pertaining to local human skeletal repositories were gathered through a combination of literature review and direct contact with local curators for information. Data pertaining to source origins, sample demographics, and temporal distribution (where applicable) were extracted and reporting trends across publications were assessed.

RESULTS

South Africa has 12 main human skeletal repositories, six affiliated with universities and six with museums. There are over 12 300 human skeletal remains housed across these repositories, mainly of cadaveric, archaeological, forensic (medico-legal), and unknown origin. Universities are primarily stewards of large cadaveric collections (n = ± 6 200); however, a few manage archaeological (n = ± 1 300) and forensic repositories (n = ± 1 000). Museums exclusively curate repositories of archaeological origin and approximately ± 3 700 archaeological individuals can be found countrywide.

CONCLUSIONS

The ethical challenges faced by South African repositories are deeply connected to the country's colonial and apartheid history. Concerns related to consent, autonomy, cultural sensitivity, data availability and the respectful treatment of the deceased, require constant attention and consideration. We highlight several initiatives undertaken to address these issues, including the implementation of new management approaches by repositories, a shift away from using unclaimed bodies, efforts in deaccessioning and repatriation and an increased focus on community engagement.

Human identification: an investigation of 3D models of paranasal sinuses to establish a biological profile on a modern UK population

Medical imaging is a valuable source for facilitating empirical research and provides an accessible gateway for developing novel forensic anthropological methods for analysis including 3D modelling. This is especially critical for the United Kingdom (UK), where methods developed from modern UK populations do not currently exist. This study introduces a new approach to assist in human identification using 3D models of the paranasal sinuses. The models were produced from a database of 500 modern CT scans provided by University College London Hospital. Linear measurements and elliptic Fourier coefficients taken from 1500 three-dimensional models across six ethnic groups assessed by one-way ANOVA and discriminant function analysis showed a range of classification rates with certain rates reaching 75-85.7% (p < 0.05) in correctly classifying age and sex according to size and shape. The findings offer insights into the potential for employing paranasal sinuses as an attribute for establishing the identification of unknown human remains in future crime reconstructions.

Population affinity estimation using pelvic measurements based on computed tomographic data acquired from Japanese and Western Australian populations

The present study analyzes morphological differences in the pelvis of Japanese and Western Australian individuals and investigates the feasibility of population affinity classification based on computed tomography (CT) data. The Japanese and Western Australian samples comprise CT scans of 207 (103 females; 104 males) and 158 (78 females; 80 males) adult individuals, respectively. Following volumetric reconstruction, a total of 19 pelvic landmarks were obtained on each sample, and 11 measurements, including two angles, were calculated. Machine learning methods (random forest modeling [RFM] and support vector machine [SVM]) were used to classify population affinity. Classification accuracy of the two-way models was approximately 80% for RFM: the two-way sex-specific and sex-mixed models for SVM achieved > 90% and > 85%, respectively. The sex-specific models had higher accurate classification rates than the sex-mixed models, except for the Japanese male sample. The classification accuracy of the four-way sex and population affinity model had an overall classification accuracy of 76.71% for RFM and 87.67% for SVM. All the correct classification rates were higher in the Japanese relative to the Western Australian sample. Our data suggest that pelvic morphology is sufficiently distinct between Japanese and Western Australian individuals to facilitate the accurate classification of population affinity based on measurements acquired in CT images. To the best of our knowledge, this is the first study investigating the feasibility of population affinity estimation based on CT images of the pelvis, which appears as a viable supplement to traditional approaches based on cranio-facial morphology.

Forensic evaluation of craniometric characteristics of the Kazakhstan population

Background

The human skull is the part of the skeleton most frequently used in population studies, as it was more exposed to genetic factors and less exposed to environmental factors. The skull is an important component in human forensic identification.

Materials and methods

The craniometric characteristics of 186 male and 114 female skulls found on the territory of Kazakhstan were studied. Dimensions were measured using standard anthropometric methods and instruments. The results of measurements of 25 craniometric parameters are presented. Methods of descriptive and parametric statistics were used.

Results

Statistical analysis showed significant regional dimorphism, confirming theindividuality of the Kazakhstan population. Statistically significant deviations werefound in 6 male craniometric characteristics and 4 female craniometric characteristics(p<0.05). The most dimorphous variables for regional identification in Kazakhstanmales were the higher skull base and frontal chord width , full face height , condylarand bigonial width , and low mandibular body reference values (p<0.05). For females,significant statistical discrepancies were seen in the transverse diameter and skullbase width, mastoid and occipital aperture width (p<0.05).

Conclusion

The recorded variations and changes in the morphology of the humanskull of the population of Kazakhstan indicate the need to develop and updateosteometric standards used in practice for specific populations. All this will significantlyimprove the accuracy of forensic identification and more fully study the biologicalpatterns of population formation, as well as evaluate the comparative effectiveness ofindividual features in the reconstruction of the population history of various populationgroups.

Estimation of ancestry from cranial measurements based on MDCT data acquired in a Japanese and Western Australian population

The estimation of ancestry is important not only towards establishing identity but also as a required precursor to facilitating the accurate estimation of other attributes such as sex, age at death, and stature. The present study aims to analyze morphological variation in the crania of Japanese and Western Australian individuals and test predictive models based on machine learning for their potential forensic application. The Japanese and Western Australian samples comprise computed tomography (CT) scans of 230 (111 female; 119 male) and 225 adult individuals (112 female; 113 male), respectively. A total of 18 measurements were calculated, and machine learning methods (random forest modeling, RFM; support vector machine, SVM) were used to classify ancestry. The two-way unisex model achieved an overall accuracy of 93.2% for RFM and 97.1% for SVM, respectively. The four-way sex and ancestry model demonstrated an overall classification accuracy of 84.0% for RFM and 93.0% for SVM. The sex-specific models were most accurate in the female samples (♀ 95.1% for RFM and 100% for SVM; ♂91.4% for RFM and 97.4% for SVM). Our findings suggest that cranial measurements acquired in CT images can be used to accurately classify Japanese and Western Australian individuals into their respective population. This is the first study to assess the feasibility of ancestry estimation using three-dimensional CT images of the skull.

Anatomical landmarks for localisation of the anterior ethmoidal artery: a combined radiological and cadaveric (endoscopic) study

PURPOSE

The anterior ethmoidal artery is a major surgical landmark that is susceptible to iatrogenic injury during surgery of the anterior ethmoidal sinus, frontal sinus, and skull base. The present study aimed to define the location of the anterior ethmoidal artery in relation to specific anatomical landmarks using radiological imaging and endoscopic dissection.

METHODS

Eighty-six anterior ethmoidal arteries were assessed using computed tomography scans (bilateral analyses) and forty anterior ethmoidal arteries were assessed using cadaveric specimens (bilateral analyses). The skull base, anterior nasal spine, anterior axilla of the middle turbinate, and nasal axilla were morphometrically analysed to determine their reliability as anterior ethmoidal artery landmarks.

RESULTS

Distances to the skull base, anterior nasal spine, and nasal axilla displayed statistically significant differences between sexes and sides (p < 0.05). All landmarks demonstrated excellent reliability as anatomical landmarks for the localisation of the anterior ethmoidal artery, radiologically and endoscopically (ICC values ranged from 0.94 to 0.99).

CONCLUSION

The middle turbinate axilla was the most reliable landmark, due to the lack of statistically significant differences according to sex and laterality, and the high inter-rater agreement between measurements. Anatomical knowledge of variations and relationships observed in the present study can be applied to surgeries of the anterior ethmoidal sinus, frontal sinus, and skull base to improve localisation of the anterior ethmoidal artery, preoperatively and intraoperatively, and avoid iatrogenic injury of the vessel.

Accuracies of discriminant function equations for sex estimation using long bones of upper extremities

One of the scopes of practice of forensic anthropologists is the estimation of sex from skeletal remains. As a result, population-specific discriminant function equations have been developed from measurements of various bones of the human skeletons. Steyn, Patriquin (Forensic Sci Int 191 (1-3):113, 2009) noted that the lack of skeletal collections and data from most parts of the world has made this process impractical. Previous attempts to develop global discriminant function equations from measurements of the pelvis showed that population-specific equations are not necessary as equations derived from other populations yielded high sex estimation scores when applied to a different population. However, information on the suitability and applicability of generalised equations in sex estimation using long bones is still scarce. It is, therefore, the aim of this study to assess the accuracies of population-specific discriminant function equations derived from measurements of long bones of the upper limb of South African population groups. Data analysed in the current study were obtained from Mokoena, Billings, Bidmos, Mazengenya (Forensic Sci Int 278:404, 2017) and Mokoena, Billings, Gibbon, Bidmos, Mazengenya (Science & Justice 6(59):660-666, 2019) in which a total sample of 988 bones (humeri, radii, and ulnae) of South Africans of African descent (SAAD), South Africans of European descent (SAED) and Mixed Ancestry South Africans (MASA) were measured. Stepwise and direct discriminant function analyses were performed on the pooled data. Each function was used to estimate the sex of cases in each population group separately and average accuracies calculated. Thereafter, population-specific discriminant function equations were formulated for each population group and then applied to other population groups. The average accuracies of functions for pooled data ranged between 80.7 and 86.5%. The cross-validation average accuracies remained unchanged for most functions, confirming the validity of derived functions. A drop in average accuracies (0.8-5.3%) was observed when the functions were tested on a sample of SAAD while increased average accuracy was observed for the SAED and MASA (0.5-6.9%). When population-specific functions for a particular population group were applied to other groups, a wide range of a drop in average accuracies was observed (1.3 to 22.4%). This thereby confirms that population-specific equations should not be applied to other population groups. However, discriminant function equations from the pooled data of South Africans are accurate in the estimation of sex and efforts should be made towards the development and validation of such equations from as many bones of the human skeleton.

Assessing zygomatic shape and size for estimating sex and ancestry in a South African sample

Unidentified, decomposed and skeletonised human remains are frequently found in South Africa, therefore, standardised, reliable and relevant sex and ancestry estimation methods are required for forensic identification. This study assessed sex and ancestral variation in zygomatic size and shape in a South African population using geometric morphometric analyses. The zygoma of 158 South African individuals were sampled. Eight zygomatic landmarks were captured in 3-dimensions using a Microscribe G2 digitiser and assessed using procrustean geometric morphometrics. Shape and size differences were analysed using multivariate linear regression, discriminant function and canonical variate analyses. Males had significantly larger zygomas than females. Significant shape variation was found between ancestral groups. Bantu-speaking and Mixed ancestry individuals had narrower, shorter and more anteriorly projecting orbital margins, whilst Europeans had vertically elongated and receded orbital margins. European ancestral groups were most discernible from Bantu-speakers and Mixed ancestral groups. Ancestry estimation accuracies improved when ancestry was aggregated with sex. Pairwise ancestry-linked comparisons in females were as follows; Bantu-speakers (76%) from Europeans (72%), Bantu-speakers (71%) from Mixed ancestry (59%) and European (72%) from Mixed ancestry (63%). Similarly, ancestry-linked comparisons in males were as follows; Bantu-speakers (77%) from Europeans (81%), Bantu-speakers (53%) from Mixed ancestry (59%) and European (72%) from Mixed ancestry (82%). Size differences are putatively linked to variations in hormone-regulated growth and muscular robusticity between males and females. Shape variations between ancestral groups are likely attributable to the heterogenous genetic and ancestral origins of the South African population. It is challenging to distinguish between South Africa Bantu speakers and Mixed ancestry people due to Mixed ancestry individuals having variable genetic contributions from Khoesan, Bantu-speakers, Europeans and Asians. Bantu-speaking and Mixed ancestry people had zygomatic morphologies consistent with historical thermoregulatory adaptations to sub-Saharan climates, reported in African-descendants. Zygomatic morphology in European descendants suggests ancestral origins from colder climatic regions. This study demonstrated the utility of the zygoma in distinguishing between ancestral groups in South Africa, but further research is required to develop population-specific standards to distinguish between South African populations with shared African ancestry. The zygoma shows a promising ability to estimate sex and ancestry in South Africans, suggesting population specific standards for this bone may be of forensic interest.

The expression of neurological soft signs in two African populations with first-episode schizophrenia

Information about patterns of expression of neurological soft signs (NSS) in schizophrenia among individuals belonging to the same genetic ancestry may provide new insight for the understanding of the disease's genetic functions. This study aimed to investigate whether patterns of NSS expression in first episode schizophrenia are comparable in populations with dissimilar genetic ancestry. A sample of 207 patients with first episode schizophrenia were examined using the Neurological Evaluation Scale before they were exposed to anti-psychotics. They were allocated to two African ancestry groups: Black (81 Yoruba Nigerians, and 18 Xhosa South Africans), and non-Black (98 Coloured, and 10 White South Africans). Assessments were carried out using validated measures of clinical characteristics of schizophrenia. We determined the frequency, severity, factor structure, and association of NSS with clinical characteristics. Factor derived categories were compared using the Pearson's ( r) and Tucker's congruence methods. The associations between factor derived categories and clinical characteristics of schizophrenia were determined using Pearson's correlations and multiple regression analyses. Neurological soft signs were more frequent and more severe in the Black African ancestry group. Also, the factor structure and presentation of NSS in the two ancestry groups were significantly different. Neurological soft signs, especially motor sequencing and cognitive-perceptual abnormalities, were independently associated with disorganization psychopathologies in all the participant groups. Differences in the profile of NSS in Black compared with non-Black African ancestry patients with first episode schizophrenia may suggest differing patterns of expression of NSS in schizophrenia according to genetic ancestry.

Morphometric Analysis of the Neurocranium in an Adult South African Cadaveric Sample

Craniometric studies of South Africans yield high accuracies of sex and ancestry classification, but most assess only inter-group variation of Black and White individuals, excluding the highly heterogeneous Colored group, which constitute a significant proportion of the population. This study applied a geometric morphometric approach to the neurocrania of 774 Black, Colored, and White individuals to assess sex and ancestry estimation accuracy based on the detected morphological variation. Accuracies of 70% and 83% were achieved for sex and ancestry, respectively, with ancestry-related variation contributing the largest proportion of overall observed variation. Even when comparing the closely related Black and Colored groups, relatively high accuracies were obtained. It is thus recommended that a similar approach be used to develop a contemporary three-dimensional database, which can be used to objectively, reliably, and accurately classify unknown remains in the South African forensic context.

Three-dimensionally derived interlandmark distances for sex estimation in intact and fragmentary crania

The skull is the element most frequently presented to forensic anthropologists for analysis yet weathering, corpse maiming, and scavenger activity often result in damage and fragmentation. This fragmentation results in a reduction in the number of traditional calliper derived measurements that can be obtained and subjected to discriminant based analyses for sex estimation. In this investigation, we employed three-dimensional geometric morphometric methods to derive novel interlandmark distance measures across six regions of the cranium including the basicranium, basipalate, zygoma, orbits and the cranium globally to create functions to discriminate sex with high efficacy, even in the event of fragmentation. Forty-five homologous landmarks were digitised across each of 227 (114 males and 113 females) South African crania of European descent (white) sampled from the Raymond A Dart Collection of Human Skeletons, housed in the School of Anatomical Sciences, University of the Witwatersrand, South Africa. A total of 990 interlandmark distances (ILDs) were mathematically derived using Pythagorean geometry. These ILDs were then filtered by region and subjected to both direct and stepwise discriminant function analyses. Discriminant equations where derived for each region and achieved the following average cross-validated sex estimation accuracies: basicranium-74%; basipalate-80.2%; zygomatic-82.4; orbits-71.8%; nasomaxilla-83.7%; global cranium-88.2%. A large number of the ILDs used to derive the discriminant functions are novel, demonstrating the efficacy of geometric morphometric methods and illustrating the need to reassess old methods of data collection using modern methods to determine whether they best capture biological differences. The results of this study provide an invaluable contribution to forensic anthropology in South Africa as it provides an accurate, practical means of assessing sex using fragmentary material that may otherwise have been disregarded. These will undeniable aid in accurate sex estimation and ultimately, victim identification.

Metric assessment of ancestry from the vertebrae in South Africans

Ancestry estimation is one of the four basic steps for developing a biological profile. Research has shown that there are a certain amount of morphological and anthropometric differences among skeletons in populations. The aim of this study was to examine the Pretoria Bone Collection to analyze the ancestral variation in the vertebrae of the South African black and white population. The sample was composed of complete vertebrae from 144 individuals (73 whites, 71 blacks). Ancestry differences were assessed using the discriminant function procedure. Regarding the results of this study, when vertebral columns were evaluated, the data indicated (with high reliability) a difference between the two ancestries. The analysis provided an accuracy rate of 98 % in males and 93.5 % in females. Compared to skeleton pieces such as the skull and the pelvis, which have been studied often with high reliability results, these rates are highly significant.

Vitamin K Dependent Protection of Renal Function in Multi-ethnic Population Studies

BACKGROUND

Following activation by vitamin K (VK), matrix Gla protein (MGP) inhibits arterial calcification, but its role in preserving renal function remains unknown.

METHODS

In 1166 white Flemish (mean age, 38.2 years) and 714 South Africans (49.2% black; 40.6 years), we correlated estimated glomerular filtration (eGFR [CKD-EPI formula]) and stage of chronic kidney disease (CKD [KDOQI stages 2-3]) with inactive desphospho-uncarboxylated MGP (dp-ucMGP), using multivariable linear and logistic regression.

RESULTS

Among Flemish and white and black Africans, between-group differences in eGFR (90, 100 and 122 mL/min/1.73 m(2)), dp-ucMGP (3.7, 6.5 and 3.2 μg/L), and CKD prevalence (53.5, 28.7 and 10.5%) were significant, but associations of eGFR with dp-ucMGP did not differ among ethnicities (P ≥ 0.075). For a doubling of dp-ucMGP, eGFR decreased by 1.5 (P = 0.023), 1.0 (P = 0.56), 2.8 (P = 0.0012) and 2.1 (P < 0.0001) mL/min/1.73 m(2) in Flemish, white Africans, black Africans and all participants combined; the odds ratios for moving up one CKD stage were 1.17 (P = 0.033), 1.03 (P = 0.87), 1.29 (P = 0.12) and 1.17 (P = 0.011), respectively.

INTERPRETATION

In the general population, eGFR decreases and CKD risk increases with higher dp-ucMGP, a marker of VK deficiency. These findings highlight the possibility that VK supplementation might promote renal health.

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

The cranium is widely recognized as the most important skeletal element to use when evaluating population differences and estimating ancestry. However, the cranium is not always intact or available for analysis, which emphasizes the need for postcranial alternatives. The purpose of this study was to quantify postcraniometric differences among South Africans that can be used to estimate ancestry. Thirty-nine standard measurements from 11 postcranial bones were collected from 360 modern black, white and coloured South Africans; the sex and ancestry distribution were equal. Group differences were explored with analysis of variance (ANOVA) and Tukey's honestly significant difference (HSD) test. Linear and flexible discriminant analysis (LDA and FDA, respectively) were conducted with bone models as well as numerous multivariate subsets to identify the model and method that yielded the highest correct classifications. Leave-one-out (LDA) and k-fold (k=10; FDA) cross-validation with equal priors were used for all models. ANOVA and Tukey's HSD results reveal statistically significant differences between at least two of the three groups for the majority of the variables, with varying degrees of group overlap. Bone models, which consisted of all measurements per bone, resulted in low accuracies that ranged from 46% to 63% (LDA) and 41% to 66% (FDA). In contrast, the multivariate subsets, which consisted of different variable combinations from all elements, achieved accuracies as high as 85% (LDA) and 87% (FDA). Thus, when using a multivariate approach, the postcranial skeleton can distinguish among three modern South African groups with high accuracy.