A New Theoretical Approach to Ancestry Estimation as Applied to Human Crania

Since Frank Livingstone proposed the idea that there are no races, only clines, in 1962, little has changed in the way that anthropologists study and, ultimately, estimate ancestry. The way in which we talk about the study of human variation may have changed--shifting away from “racial” labels and towards those of supposed ancestral origins--but the methods with which we label and analyze groups, however termed, has remained the same. In this paper, I suggest a new theoretical approach to ancestry estimation that does not rely on group labels using Howells Craniometric dataset as an example. In the suggested workflow, the data structure themselves into natural clusters, which I am referring to as Morphogroups, without the reliance of a group label. Each Morphogroup is explored for sub-groups and the process is repeated until no further distinctions can be made. At each level an individual is compared to the Morphogroup in a descriptive manner focusing on similarities and differences. Lastly, a multi-iteration classification procedure, using random forest modeling, is implemented to classify by Morphogroup. In this test, hierarchical clustering was used to identify the optimal number of natural clusters within the data and principal components analysis was used to explore Morphogroups. Using my suggested workflow, three main Morphogroups were identified with each having different numbers of subclusters ranging from 0-8. Morphogroup correct classifications are typically in the mid 90 percent and the accompanying sex estimations between 93-100% correct. Additionally, for anyone who has access to R, I have provided a markdown file that shows all of the code used for this paper step-by-step at https://rpubs.com/kenyhercz2/717620. I want to make it clear this is not the way I think this should be done, rather one of myriad ways it could be done. Human variation and identity are not static and we need to stop thinking of them as such. It is on us to help one another get better at rethinking and redefining what is possible for our field

Molar size and shape in the estimation of biological affinity: a comparison of relative cusp locations using geometric morphometrics and interlandmark distances

Thesis (Ph.D.) University of Alaska Fairbanks, 2014The study of teeth has been a central tenet in biological anthropology since the inception of the field. Teeth have been previously shown to have a high genetic component. The high heritability of teeth has allowed researchers to use them to answer a myriad of anthropological questions ranging from human origins to modern variation due to microevolution. Traditionally, teeth have been studied either morphologically, through the assignment of nonmetric character states, or metrically, through mesiodistal and buccolingual crown measures. Increasingly, geometric morphometric techniques are being used to answer anthropological questions, especially dentally. However, regardless of analytical technique utilized, the biological affinity of modern U.S. individuals has often been limited to examination under a forensic lens (classification of either American Asian, black, Hispanic, or white) without consideration of parent populations. The current study uses geometric morphometric techniques on human molars for two main goals: 1) to examine biological affinity of each of the four largest population groups in regard to population history; and 2) examine the variation within and among the four modern groups as a means of classification. A total of 1,225 dentitions were digitized. Each of the four modern U.S. groups was compared to possible parental groups via discriminant function analysis (DFA). Additionally affinity was examined using Mahalanobis generalized distances (D²) wherein significance of distances between groups was calculated via permutation tests. Furthermore, the D² values were subjected to principal coordinate analysis, or classical multidimensional scaling, to visualize group similarity and dissimilarity. Each group demonstrated affinity with potential parental groups and geographically similar groups as expected given population histories; however, each was also significantly unique from the comparison groups. The four modern U.S. groups were then compared to one another using the same statistical tests. Total among-group correct classifications ranged from 33.9-55.5%, indicating a greater classification than random chance (25%). These classifications were negatively correlated with the reported intermarriage rates for each group: American whites and blacks have the lowest intermarriage rates, which resulted in the highest correct classifications. Conversely, American Asians and Hispanics have the highest intermarriage rates, which resulted in the lowest total correct classifications. Still, the DFA model created from the modern U.S. sample was able to accurately classify a holdout sample. Lastly, a comparison of the three most abundant groups in the U.S. (black, Hispanic, and white), achieved a total correct classification of 72.3%, which is comparable to other studies focusing on the same populations. Restricted gene flow through sociologically constructed barriers and positive assortative mating are the likely factors in the observed variation.Chapter 1: Introductions -- 1.1 Dental development -- 1.1.1 Molar eruption timing -- 1.2.1 The field concept model -- 1.2.2 The clone model -- 1.2.3 The homeobox model -- 1.2.4 Combined models -- 1.3 Studies of dental morphology -- 1.4 Studies of odontometry -- 1.5 Studies of dental geometric morphometrics -- 1.6 Summary -- 1.7 Dissertation outline -- Chapter 2: Concept of race, biological affinity, social identity, and population histories in the United States -- 2.1 Modern U.S. population history -- 2.1.1 Population history of American whites -- 2.1.1.1 English -- 2.1.1.2 Irish -- 2.1.1.3 German -- 2.1.1.4 Jewish -- 2.1.1.5 Italian -- 2.1.2 Population history of American blacks -- 2.1.3 Population history of American Asians -- 2.1.3.1 Chinese -- 2.1.3.2 Japanese -- 2.1.3.3 Filipinos, Koreans, and Vietnamese -- 2.1.4 Population history of American Hispanics -- 2.1.4.1 Mexican -- 2.1.4.2 Puerto Rican -- 2.1.4.3 Cuban -- 2.2 Discussion -- 2.3 Summary -- Chapter 3: Materials and methods -- 3.1 Samples -- 3.1.1 Modern American -- 3.1.2 Historic parental groups -- 3.1.3 Modern comparison groups -- 3.2 Three-dimensional data collection -- 3.2.1 Geometric morphometrics -- 3.2.2 Data collection and preparation protocol -- 3.3 Statistics -- 3.3.1 Descriptive statistics -- 3.3.2 Principal components analysis -- 3.3.3 Discriminant function analysis -- 3.3.4 Principal coordinate analysis/classical multidimensional scaling -- 3.4 Data processing protocol summary -- 3.5 Discussion -- 3.6 Summary -- Chapter 4: Repeatability, sexual dimorphism, and asymmetry -- 4.1 Repeatability -- 4.2 Sexual dimorphism -- 4.3 Asymmetry -- 4.4 Discussion -- 4.5 Summary -- Chapter 5: Modern American Asian comparison -- 5.1 Maxillary first molar (M¹) -- 5.1.1 Descriptive statistics of principal components of shape -- 5.1.2 Principal components of shape -- 5.1.3 Interlandmark distances (ILDs) -- 5.1.4 Principal components of ILDs -- 5.2 Maxillary second molar (M²) -- 5.2.1 Descriptive statistics of principal components of shape -- 5.2.2 Principal components of shape -- 5.2.3 Interlandmark distances (ILDs) -- 5.2.4 Principal components of ILDs -- 5.3 Mandibular first molar (M¹) -- 5.3.1 Descriptive statistics of principal components of shape -- 5.3.2 Principal components of shape -- 5.3.3 Interlandmark distances (ILDs) -- 5.3.4 principal components of ILDs -- 5.4 mandibular second molar (m2) -- 5.4.1 Descriptive statistics of principal components of shape -- 5.4.2 Principal components of shape -- 5.4.3 Interlandmark distances (ILDs) -- 5.4.4 Principal components of ILDs -- 5.5 Combined molars -- 5.5.1 Discriminant function analysis -- 5.5.2 Principal coordinate analysis -- 5.6 Discussion -- 5.7 Summary -- Chapter 6: Modern American Black comparison -- 6.1 Maxillary first molar (M¹) -- 6.1.1 Descriptive statistics of principal components of shape -- 6.1.2 Principal components of shape -- 6.1.3 Interlandmark Distances (ILDs) -- 6.1.4 Principal components of ILDs -- 6.2 Maxillary second molar (M²) -- 6.2.1 Descriptive statistics of principal components of shape -- 6.2.2 Principal components of shape -- 6.2.3 Interlandmark distances (ILDs) -- 6.2.4 Principal components of ILDs -- 6.3 Mandibular first molar (M¹) -- 6.3.1 Descriptive statistics of principal components of shape -- 6.3.2 Principal components of shape -- 6.3.3 Interlandmark distances (ILDs) -- 6.3.4 Principal components of ILDs -- 6.4 Mandibular second molar (M²) -- 6.4.1 Descriptive statistics of principal components of shape -- 6.4.2 Principal components of shape -- 6.4.3 Interlandmark distances (ILDs) -- 6.4.4 Principal components of ILDs -- 6.5 Combined molars -- 6.5.1 Discriminant function analysis -- 6.5.2 Principal coordinate analysis -- 6.6 Discussion -- 6.7 Summary -- Chapter 7: Modern american hispanic comparison -- 7.1 Maxillary first molar (M¹) -- 7.1.1 Descriptive Statistics of Principal Components of Shape -- 7.1.2 Principal Components of Shape -- 7.1.3 Interlandmark distances (ILDs) -- 7.1.4 Principal components of ILDs -- 7.2 Maxillary second molar (M²) -- 7.2.1 Descriptive statistics of principal components of shape -- 7.2.2 Principal components of shape -- 7.2.3 Interlandmark distances (ILDs) -- 7.2.4 Principal Components of ILDs -- 7.3 Mandibular first molar (M¹) -- 7.3.1 Descriptive statistics of principal components of shape -- 7.3.2 Principal components of shape -- 7.3.3 Interlandmark distances (ILDs) -- 7.3.4 Principal components of the interlandmark distances -- 7.4 Mandibular second molar (M²) -- 7.4.1 Descriptive statistics of principal components of shape -- 7.4.2 Principal components of shape -- 7.4.3 Interlandmark distances (ILDs) -- 7.4.4 Principal components of ILDs -- 7.5 Combined Molars -- 7.5.1 Discriminant function analysis -- 7.5.2 Principal coordinate analysis -- 7.6 Discussion -- 7.7 Summary -- Chapter 8: Modern American white comparison -- 8.1 Maxillary first molar (M¹) -- 8.1.1 Descriptive statistics of principal components of shape -- 8.1.2 Principal components of shape -- 8.1.3 Interlandmark distances (ILDs) -- 8.1.4 Principal components of ILDs -- 8.2 Maxillary second molar (M²) -- 8.2.1 Descriptive statistics of principal components of shape -- 8.2.2 Principal components of shape -- 8.2.3 Interlandmark distances (ILDs) -- 8.2.4 Principal components of ILDs -- 8.3 Mandibular first molar (M¹) -- 8.3.1 Descriptive statistics of principal components of shape -- 8.3.2 Principal components of shape -- 8.3.3 Interlandmark distances (ILDs) -- 8.3.4 Principal components of ILDs -- 8.4.1 Descriptive statistics of principal components of shape -- 8.4.2 Principal components of shape -- 8.4.3 Interlandmark distances (ILDs) -- 8.4.4 Principal components of ILDs -- 8.5 Combined molars -- 8.5.1 Discriminant function analysis -- 8.5.2 Principal coordinate analysis -- 8.6 Discussion -- 8.7 Summary -- Chapter 9: Comparison of modern American groups -- 9.1 Maxillary first molar (M¹) -- 9.1.1 Descriptive statistics of principal components of shape -- 9.1.2 Principal components of shape -- 9.1.3 Interlandmark distances (ILDs) -- 9.1.4 Principal components of ILDs -- 9.2 Maxillary second molar (M²) -- 9.2.1 Descriptive statistics of principal components of shape -- 9.2.2 Principal components of shape -- 9.2.3 Interlandmark distances (ILDs) -- 9.2.4 Principal components of ILDs -- 9.3 Mandibular first molar (M¹) -- 9.3.1 Descriptive statistics of principal components of shape -- 9.3.2 Principal components of shape -- 9.3.3 Interlandmark distances (ILDs) -- 9.3.4 Principal components of ILDs -- 9.4 Mandibular second molar (M²) -- 9.4.1 Descriptive statistics of principal components of shape -- 9.4.2 Principal components of shape -- 9.4.3 Interlandmark distances (ILDs) -- 9.4.4 Principal components of ILDs -- 9.5 Combined molars -- 9.6 Discriminant function analysis -- 9.7 Principal coordinate analysis -- 9.8 An applied example -- 9.9 Three group classification example -- 9.10 Discussion -- 9.11 Summary -- Chapter 10: Discussion -- 10.1 Repeatability, Sexual Dimorphism, and Asymmetry -- 10.1.1 Repeatability -- 10.1.2 Sexual dimorphism -- 10.1.3 Asymmetry -- 10.2 American Asian comparison -- 10.1.3 Asymmetry -- 10.2 American Asian comparison -- 10.3 American Black comparison -- 10.4 American Hispanic comparison -- 10.5 American White comparison -- 10.6 Comparison of modern American groups -- 10.6.1 Shape -- 10.6.2 Size -- 10.6.3 Shape and size -- 10.6.4 Individual molar variability -- 10.6.5 Comparison to other research in U.S. biological affinity -- 10.7. Biological affinity in the United States -- Chapter 11: Conclusions -- 11.1 Repeatability, sexual dimorphism, and asymmetry -- 11.2 American Asian population comparison -- 11.3 American Black population comparison -- 11.4 American Hispanic population comparison -- 11.5 American White population comparison -- 11.6 Comparison of modern American groups -- 11.7. Future implications -- References -- Appendices

Grave mapping in support of the search for missing persons in conflict contexts

We review the current and potential uses of Geographic Information Software (GIS) and “spatial thinking” for understanding body disposal behaviour in times of mass fatalities, particularly armed conflict contexts. The review includes observations made by the authors during the course of their academic research and professional consulting on the use of spatial analysis and GIS to support Humanitarian Forensic Action (HFA) to search for the dead, theoretical and statistical considerations in modelling grave site locations, and suggestions on how this work may be advanced further.The International Committee of the Red Crosshttp://www.elsevier.com/locate/forsciint2018-09-30hj2017Anatom

An evaluation of nasal bone and aperture shape among three South African populations

Reliable and valid population specific standards are necessary to accurately develop a biological profile, which includes an estimation of peer-reported social identification (Hefner, 2009). During the last 300 years, colonialism, slavery and apartheid created geographic, physical and social divisions of population groups in South Africa. The purpose of this study was to evaluate variation in nasal bone and aperture shape in a modern population of black, white, and coloured South Africans using standard craniometric variables and geometric morphometrics, namely general Procrustes and elliptical Fourier analyses. Fourteen standard landmarks were digitally recorded or computationally derived from 310 crania using a 3D coordinate digitizer for discriminant function, principal components and generalized Procrustes analyses. For elliptical Fourier analysis, outlines of the nasal aperture were generated from standardized photographs. All classification accuracies were better than chance; the lowest accuracies were for coloured and the highest accuracies were for white South Africans. Most difficulties arose in distinguishing coloured and black South African groups from each other. Generally, misclassifications were noted between the sexes within each group rather than among groups, which suggests that sex has less influence on nasal bone and aperture shape than ancestry. Quantifiable variation in shape of the nasal aperture region between white and non-white South African groups was observed.National Research Foundation of South Africa (NRF)http://www.elsevier.com/locate/forsciint2016-07-30hb201

Sexual dimorphism in cranial morphology among modern South Africans

Pattern expressions of morphoscopic cranial traits vary across populations with classification accuracies being highly dependent on the reference collection to which unknown skulls are compared. Despite recent developments in populationspecific standards for South Africans, researchers have not addressed the accuracy of morphological methods. Several studies demonstrate differences in sexual dimorphism between South Africans and North Americans, warranting a need to re-evaluate sex estimation methods in South Africa. The purposes of this study were to test the reliability and accuracy of the Walker (2008) method and to examine patterns of sexual dimorphism among South Africans. A total of 245 modern Black and White South African male and female crania from the Pretoria Bone Collection, University of Pretoria, were scored using theWalker (2008) methodology. Cohen’s kappa was used to evaluate reliability of the method, and percent correct assessed validity of the method. Logistic regression was utilised to create modified population-specific formulae. Inter- and intra-observer agreement was moderate to excellent (0.60–0.90), except for the mental eminence (0.40). The percent correct results for sex were 80%or higher for combinations of glabella,mastoid andmenton and between 68 % and 73 % for menton, mastoid, orbital and nuchal margin using logistic equations of Walker (2008). White males had the highest (94–97 %) and White females had the lowest (31–62 %) percent correct. The low accuracies obtained when using Walker’s (2008) equations emphasised the need for population-specific sex estimation models. Modified formulae for South Africans were created, yielding higher classification rates (84–93 %) than when North American standards were employed.National Research Foundation (NRF)http://link.springer.com/journal/4142016-07-31hb201

Molar size and shape in the estimation of biological affinity: A comparison of relative cusp locations using geometric morphometrics and interlandmark distances

The study of teeth has been a central tenet in biological anthropology since the inception of the field. Teeth have been previously shown to have a high genetic component. The high heritability of teeth has allowed researchers to use them to answer a myriad of anthropological questions ranging from human origins to modern variation due to microevolution. Traditionally, teeth have been studied either morphologically, through the assignment of nonmetric character states, or metrically, through mesiodistal and buccolingual crown measures. Increasingly, geometric morphometric techniques are being used to answer anthropological questions, especially dentally. However, regardless of analytical technique utilized, the biological affinity of modern U.S. individuals has often been limited to examination under a forensic lens (classification of either American Asian, black, Hispanic, or white) without consideration of parent populations. The current study uses geometric morphometric techniques on human molars for two main goals: 1) to examine biological affinity of each of the four largest population groups in regard to population history; and 2) examine the variation within and among the four modern groups as a means of classification. A total of 1,225 dentitions were digitized. Each of the four modern U.S. groups was compared to possible parental groups via discriminant function analysis (DFA). Additionally affinity was examined using Mahalanobis generalized distances (D2) wherein significance of distances between groups was calculated via permutation tests. Furthermore, the D2 values were subjected to principal coordinate analysis, or classical multidimensional scaling, to visualize group similarity and dissimilarity. Each group demonstrated affinity with potential parental groups and geographically similar groups as expected given population histories; however, each was also significantly unique from the comparison groups. The four modern U.S. groups were then compared to one another using the same statistical tests. Total among-group correct classifications ranged from 33.9-55.5%, indicating a greater classification than random chance (25%). These classifications were negatively correlated with the reported intermarriage rates for each group: American whites and blacks have the lowest intermarriage rates, which resulted in the highest correct classifications. Conversely, American Asians and Hispanics have the highest intermarriage rates, which resulted in the lowest total correct classifications. Still, the DFA model created from the modern U.S. sample was able to accurately classify a holdout sample. Lastly, a comparison of the three most abundant groups in the U.S. (black, Hispanic, and white), achieved a total correct classification of 72.3%, which is comparable to other studies focusing on the same populations. Restricted gene flow through sociologically constructed barriers and positive assortative mating are the likely factors in the observed variation

Ancestry estimation in South Africa using craniometrics and geometric morphometrics

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 craniometric data. 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.National Research Foundation of South Africa (NRF).http://www.elsevier.com/locate/forsciinthb201

Examining interobserver reliability of metric and morphoscopic characteristics of the mandible

Mandibular metric and morphological characteristics have long been used for sex and ancestry estimation. Currently, there are no large‐scale studies examining interobserver agreement, particularly examining the role of observer experience. This study examines the interobserver agreement of six morphoscopic and eleven metric mandibular variables. Four observers with varied levels of experience scored 183 mandibles from the William M. Bass Donated Skeletal Collection. Absolute agreement and consistency were evaluated with the intraclass correlation coefficient (ICC). Additionally, technical error of measurement (TEM) and relative TEM (%TEM) were calculated for each metric variable. All analyses were conducted twice—once with all observers and again with only experienced observers. Results show mean morphoscopic agreement of 0.543 among all observers and 0.615 for experienced observers, and mean metric agreement of 0.886 among all observers and 0.911 for experienced observers. Further, no TEM exceeded 2 mm. All results were significant (p < 0.001).Presented in part at the 68th Annual Meeting of the American Academy of Forensic Sciences, February 22–27, 2016, in Las Vegas, NV.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1556-4029hj2018Anatom

Sexual dimorphism in cranial morphology among modern South Africans

Pattern expressions of morphoscopic cranial traits vary across populations with classification accuracies being highly dependent on the reference collection to which unknown skulls are compared. Despite recent developments in populationspecific standards for South Africans, researchers have not addressed the accuracy of morphological methods. Several studies demonstrate differences in sexual dimorphism between South Africans and North Americans, warranting a need to re-evaluate sex estimation methods in South Africa. The purposes of this study were to test the reliability and accuracy of the Walker (2008) method and to examine patterns of sexual dimorphism among South Africans. A total of 245 modern Black and White South African male and female crania from the Pretoria Bone Collection, University of Pretoria, were scored using theWalker (2008) methodology. Cohen’s kappa was used to evaluate reliability of the method, and percent correct assessed validity of the method. Logistic regression was utilised to create modified population-specific formulae. Inter- and intra-observer agreement was moderate to excellent (0.60–0.90), except for the mental eminence (0.40). The percent correct results for sex were 80%or higher for combinations of glabella,mastoid andmenton and between 68 % and 73 % for menton, mastoid, orbital and nuchal margin using logistic equations of Walker (2008). White males had the highest (94–97 %) and White females had the lowest (31–62 %) percent correct. The low accuracies obtained when using Walker’s (2008) equations emphasised the need for population-specific sex estimation models. Modified formulae for South Africans were created, yielding higher classification rates (84–93 %) than when North American standards were employed.National Research Foundation (NRF)http://link.springer.com/journal/4142016-07-31hb201

Internal tooth structure and burial practices: insights into the Neolithic necropolis of Gurgy (France, 5100-4000 cal. BC)

Variations in the dental crown form are widely studied to interpret evolutionary changes in primates as well as to assess affinities among human archeological populations. Compared to external metrics of dental crown size and shape, variables including the internal structures such as enamel thickness, tissue proportions, and the three-dimensional shape of enamel-dentin junction (EDJ), have been described as powerful measurements to study taxonomy, phylogenetic relationships, dietary, and/or developmental patterns. In addition to providing good estimate of phenotypic distances within/across archeological samples, these internal tooth variables may help to understand phylogenetic, functional, and developmental underlying causes of variation. In this study, a high resolution microtomographic-based record of upper permanent second molars from 20 Neolithic individuals of the necropolis of Gurgy (France) was applied to evaluate the intrasite phenotypic variation in crown tissue proportions, thickness and distribution of enamel, and EDJ shape. The study aims to compare interindividual dental variations with burial practices and chronocultural parameters, and suggest underlying causes of these dental variations. From the non-invasive characterization of internal tooth structure, differences have been found between individuals buried in pits with alcove and those buried in pits with container and pits with wattling. Additionally, individuals from early and recent phases of the necropolis have been distinguished from those of the principal phase from their crown tissue proportions and EDJ shape. The results suggest that the internal tooth structure may be a reliable proxy to track groups sharing similar chronocultural and burial practices. In particular, from the EDJ shape analysis, individuals buried in an alcove shared a reduction of the distolingual dentin horn tip (corresponding to the hypocone). Environmental, developmental and/or functional underlying causes might be suggested for the origin of phenotypic differences shared by these individuals buried in alcoves