Testing the accuracy of the DRNNAGE software for age estimation in a modern Greek sample.

Estimation of age-at-death from human skeletal remains is fundamental in forensic anthropology as part of the construction of the biological profile of the individual under study. At the same time, skeletal age-at-death estimation in adults is problematic due to the disparity between chronological and biological age, the important inter-individual variability at the rate of skeletal aging, and inherent biases in the available methodologies (e.g., age mimicry). A recent paper proposed a method for skeletal age-at-death estimation based on multiple anatomical traits and machine learning. A software was also created, DRNNAGE, for the easy implementation of this method. The authors of that study supported that their methods have very high repeatability and reproducibility, and the mean absolute error of the age estimation was ~6 years across the entire adult age span, which is particularly high and promising. This paper tests the proposed methodology on a modern documented Greek sample of 219 adult individuals from the Athens Collection, with age-at-death from 19 to 99 years old. The sample was split into males and females as well as into individuals under and over 50 years old. We also divided the sample in 10-year intervals. First, intra- and inter-observer error was estimated in order to assess repeatability and reproducibility of the variables employed for age-at-death estimation. Then, the validity (correct classification performance) of DRNNAGE for each anatomical region individually, as well as all combined, was evaluated on each demographic separately and on the pooled sample. According to the results, some of the variables showed very low repeatability and reproducibility, thus their use should be cautious. The DRNNAGE software showed overall highly accurate age-at-death estimates for individuals older than 50 years, but poor on younger adults, with only exception the cranial sutures, which performed surprisingly well for all age groups. Overall, these results support the importance of cross-validation and the use of population-specific methods in forensic anthropology.

Advancements in sex estimation using the diaphyseal cross-sectional geometric properties of the lower and upper limbs.

This paper introduces an automated method for estimating sex from the lower and upper limbs based on diaphyseal CSG properties. The proposed method was developed and evaluated using 389 femurs, 412 tibias, and 404 humeri of adult individuals from a modern Greek reference sample, the Athens Collection. The skeletal properties, which were extracted with the CSG-Toolkit, were analyzed with step-wise DFA (evaluated with LOOCV) and subsequently with RBF kernel SVM supervised learning. SVM cross-validation was based on a 20-fold stratified random sample splitting as well as a chronological split based on year of birth to further assess the effect of secular change in sex estimation capacity. Maximum cross-validated classification accuracy from step-wise DFA reached 94.8% for the femur, 94.7% for the tibia, and 97.3% for the humerus, whereas SVM cross-validated results were similar although slightly lower, mainly due to the more strict cross-validation scheme. Our results suggest that the proposed sex estimation method is reasonably robust to secular change, since there was limited loss in classification accuracy between different chronological groups, despite the presence of secular change in stature of the Greek population during the examined period. The proposed method has been implemented as a function for the GNU Octave environment, named estimate_sex, which comprises a self-intuitive graphical user interface for facilitating sex estimation and is freely available under a suitable license.

Forensic sex estimation using the vertebrae: an evaluation on two European populations.

Sex estimation is one of the primary steps for constructing the biological profile of skeletal remains leading to their identification in the forensic context. While the pelvis is the most sex diagnostic bone, the cranium and other post-cranial elements have been extensively studied. Earlier research has also focused on the vertebral column with varying results regarding its sex classification accuracy as well as the underlying population specificity. The present study focuses on three easily identifiable vertebrae, namely T1, T12, and L1, and utilizes two modern European populations, a Greek and a Danish, to evaluate their forensic utility in sex identification. To this end, 865 vertebrae from 339 individuals have been analyzed for sexual dimorphism by further evaluating the effects of age-at-death and population affinity on its expression. Our results show that T1 is the best sex diagnostic vertebra for both populations reaching cross-validated accuracy of almost 90%, while age-at-death has limited effect on its sexual dimorphism. On the contrary, T12 and L1 produced varying results ranging from 75 to 83% accuracy with the Greek population exhibiting distinctively more pronounced sexual dimorphism. Additionally, age-at-death had significant effect on sexual dimorphism of T12 and L1 and especially in the Greek female and Danish male groups. Our results on inter-population comparison suggest that vertebral sex discriminant functions, and especially those utilizing multiple measurements, are highly population specific and optimally suitable only for their targeted population. An open-source software tool to facilitate classifying new cases based on our results is made freely available to forensic researchers.

Advanced procedures for skull sex estimation using sexually dimorphic morphometric features.

This paper introduces an automated method for estimating sex from cranial sex diagnostic traits by extracting and evaluating specialized morphometric features from the glabella, the supraorbital ridge, the occipital protuberance, and the mastoid process. The proposed method was developed and evaluated using two European population samples, a Czech sample comprising 170 crania reconstructed from anonymized CT scans and a Greek sample of 156 crania from the Athens Collection. It is based on a fully automatic algorithm applied on 3D models for extracting sex diagnostic morphometric features which are further processed by computer vision and machine learning algorithms. Classification accuracy was evaluated in a population specific and a population generic 2-way cross-validation scheme. Population-specific accuracy for individual morphometric features ranged from 78.5 to 96.7%, whereas population generic correct classification ranged from 71.7 to 90.8%. Combining all sex diagnostic traits in multi-feature sex estimation yielded correct classification performance in excess of 91% for the entire sample, whereas the sex of about three fourths of the sample could be determined with 100% accuracy according to posterior probability estimates. The proposed method provides an efficient and reliable way to estimate sex from cranial remains, and it offers significant advantages over existing methods. The proposed method can be readily implemented with the skullanalyzer computer program and the estimate_sex.m GNU Octave function, which are freely available under a suitable license.

A three-dimensional digital microscopic investigation of entheseal changes as skeletal activity markers.

OBJECTIVES: The current article explores the effectiveness of entheseal changes (EC) as skeletal activity markers by testing the correlation between such changes and cross-sectional geometric (CSG) properties while controlling for the effect of age and body size. MATERIALS AND METHODS: The originality of the article lies in capturing EC in a continuous quantitative manner using three-dimensional microscopy. Roughness and bone resorption were recorded on Zones 1 and 2 of three humeral entheses (subscapularis, supraspinatus, and infraspinatus) in a documented sample of 29 male skeletons. RESULTS: Our analysis found that merely 5.91% of the partial correlations between EC and CSG properties were statistically significant. In addition, two unexpected patterns were identified, namely a higher number of significant correlations on the left side entheses compared to the right side ones, and a higher number of correlations between minimum roughness and CSG properties compared to mean and maximum roughness. DISCUSSION: These patterns are the inverse of what we would expect if activity had exerted an important effect on EC expression. Therefore, they support the lack of association between EC and habitual activity, even though various factors potentially affecting the above results are discussed.

Investigating the sex-related geometric variation of the human cranium.

Accurate sexing methods are of great importance in forensic anthropology since sex assessment is among the principal tasks when examining human skeletal remains. The present study explores a novel approach in assessing the most accurate metric traits of the human cranium for sex estimation based on 80 ectocranial landmarks from 176 modern individuals of known age and sex from the Athens Collection. The purpose of the study is to identify those distance and angle measurements that can be most effectively used in sex assessment. Three-dimensional landmark coordinates were digitized with a Microscribe 3DX and analyzed in GNU Octave. An iterative linear discriminant analysis of all possible combinations of landmarks was performed for each unique set of the 3160 distances and 246,480 angles. Cross-validated correct classification as well as multivariate DFA on top performing variables reported 13 craniometric distances with over 85% classification accuracy, 7 angles over 78%, as well as certain multivariate combinations yielding over 95%. Linear regression of these variables with the centroid size was used to assess their relation to the size of the cranium. In contrast to the use of generalized procrustes analysis (GPA) and principal component analysis (PCA), which constitute the common analytical work flow for such data, our method, although computational intensive, produced easily applicable discriminant functions of high accuracy, while at the same time explored the maximum of cranial variability.

Secular change in adult stature of modern Greeks.

OBJECTIVES: In Greece, during the late 19th and early 20th century, the rural population adopted a more or less urban lifestyle. Furthermore, the first half of the 20th century finds Greece involved in five major wars, including a civil war, and consequent financial deprivation. This study investigates how the socioeconomic changes in Greece, during this period of time, have affected the stature of its population. METHODS: The Athens collection constitutes our sample with 189 adult individuals (104 males and 85 females). Stature was estimated with regression equations and secular change was evaluated by linear regression of stature with respect to the year of birth. Further analysis of our population sample was based on three time periods to explore the correlation between secular change and historical events. RESULTS: From 1879 to 1965, stature increased for both males and females. The subsequent analysis among different periods revealed that the male group exhibited a small although non-significant decline in stature during the years 1912 to 1950, which coincides with the long inter-war period. However, females appear less affected by the consequent deprivation. CONCLUSIONS: Our findings are consistent with earlier studies based on a much smaller time span. The negative effect of the economic and nutritional deprivation on stature as a result of warfare is apparent in our sample, at least for males. Furthermore, the positive effect of economic growth on stature is prominent for the entire population in the postwar period.

Age-related changes in the craniofacial region in a modern Greek population sample of known age and sex.

The aim of this paper is to investigate ageing changes in craniofacial region in both sexes and evaluate whether these shape changes are substantial to achieve age discrimination of samples used in anthropological analyses. The study sample consisted of 157 crania of known sex and age (81 males and 76 females) belonging to individuals who lived in Greece during the twentieth century. The sample was divided in three age groups: young adults (YA, 18-39 years old), middle adults (MA, 40-59 years old) and old adults (OA, >60 years old). The three-dimensional coordinates of 31 ecto-cranial landmarks were digitized using a Microscribe 3DX contact digitizer, and landmark configurations were analyzed using the generalized least-squares Procrustes method. The results indicate that both males and females show significant difference among the age groups; however, shape differences can not be used for age group discrimination due to a large range on the accuracy of age group classification. The morphometric changes related to age were different between sexes.

Cranium asymmetry in a modern Greek population sample of known age and sex.

The aim of this paper is to evaluate and quantify cranium asymmetry, sexual differences in the set of individual asymmetry scores, and the relationship between fluctuating asymmetry and age, in a modern Greek population sample. In addition, we test for the developmental origins of health and disease hypothesis by assessing the correlation between fluctuating asymmetry and cause of death. The study sample consisted of 173 crania of known sex and adult age (92 males, 81 females) belonging to individuals who lived in Greece during the twentieth century. The three-dimensional coordinates of 77 ectocranial landmarks were digitized using a Microscribe 3DX contact digitizer and landmark configurations were analyzed using the generalized least-squares Procrustes method. Regarding directional asymmetry, the results show that the human skull has a tendency for a left-side excess for the Greek population. No significant directional asymmetry differences between the sexes are found. The highest levels of fluctuating asymmetry for both sexes are located on the skull base. The levels of fluctuating asymmetry in all cranial regions appear higher for males than females. Nevertheless, these differences do not present any statistical significance between sexes. Additionally, there is no relationship between fluctuating asymmetry scores and age for both males and females. Finally, the results of this study could not confirm that early development has a significant impact on adult health outcomes.

Stature estimation equations from fragmentary long bones based on a modern Eastern Mediterranean assemblage.

Stature estimation is central in forensic anthropology and very important in bioarchaeology. For this reason, several different methods have been proposed, employing different skeletal elements and statistical approaches. A major issue with skeletonized individuals is that their bones are often found fragmented, a taphonomic parameter that limits the application of many available methods. As a result, attempts have been made to create equations to predict either directly stature or long bone length (which can then be used with current stature prediction equations) from bone fragments. The current paper is a contribution in this direction. The femur, tibia and humerus of 76 individuals from a modern Greek skeletal collection were divided into different segments using a landmark approach. Subsequently, univariate and multivariate equations were created to predict both maximum long bone length and stature from the "bone fragments". The models varied in performance depending on the specific bone fragment used, the number of variables simultaneously employed for prediction and the sex of the individuals. Although the models used to directly predict stature from bone fragment dimensions should be treated cautiously because the stature of the assemblage from the Athens Collection had itself been anatomically estimated, the results are valuable towards highlighting the complex association between bone dimensions, long bone length and living/estimated stature.

The impact of age on the morphology of the 12th thoracic vertebral endplates.

The current article explores the aging effects on the overall morphology of the endplates of the 12th thoracic vertebra (T12), while screening for sex differences. It further evaluates the suitability of T12 for estimating age-at-death in bioarcheaological contexts. We captured the morphology of the vertebral endplates, including the formation of osteophytes, in a novel continuous quantitative manner using digital photography. 168 Greek adults from the Athens Collection were used for modeling the aging effects and another 107 individuals from two Danish archaeological assemblages for evaluation. Regression analysis is based on generalized additive models for correlating age-at-death and morphological variation. Our proposed measurement method is highly reliable (R>0.98) and the main differences observed between sexes are size related. Aging has considerable effect on the endplate morphology of the T12 with the total area of the endplate, the area of the epiphyseal rim, and the shape irregularities of the endplate's external boundary being mostly affected. Multivariate regression shows that aging effects account up to 46% of the observed variation, although with differential expression between sexes. Correct age prediction on archaeological remains reached 33% with a prominent tendency for overestimation. The morphology of the T12 endplates is influenced by age and it can provide some insight with respect to the age-at-death of unidentified individuals, especially when other skeletal age markers are unavailable. Our proposed method provides an age-estimation framework for bioarchaeological settings, especially for estimating broader age ranges, such as discriminating between young and old adults.

A genetic probe into the ancient and medieval history of Southern Europe and West Asia.

Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom's northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.

Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia.

We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.

The genetic history of the Southern Arc: A bridge between West Asia and Europe.

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra-West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

Integration patterns of the asymmetric components of the skull: A covariational statistical approach on a modern Greek sample.

Objectives: The integration patterns of the asymmetric components of the skull can be informative, especially in the diagnosis and surgical treatment planning of patients. This research aims to explore the interactions of the asymmetric components between the mandible, the basicranium, and the upper face. Material and methods: The sample comprises 100 skulls of Greek adults and the three-dimensional coordinates of 35 landmarks, extracted from the cranial and mandibular virtual 3D bones, were analyzed using the generalized least-squares Procrustes method. The integration patterns of the asymmetric components of the shapes of the specific structures were evaluated through partial least-squares correlation analysis with a two-blocks approach. Results: When handling the skull regions separately, there is statistically significant integration of the asymmetric components between the mandible and the basicranium as well as between the mandible and the upper face. Furthermore, the mandible and the basicranium exhibit the strongest interaction among the three pairs examined. Conclusions: The asymmetric variation of the skull regions should be taken into consideration for surgical treatment planning. However, comparing our findings with other studies revealed that the utilization of the skull regions in the context of a structure as a whole while running the analysis, as well as different landmark combinations, may lead to different results. Furthermore, there might be population-specificity to certain integration patterns of the asymmetric component of the total shape variation among skull regions. Hence, surgical bone restoration, especially in the mandible, should consider overall skull asymmetry and population-specific data to ensure optimal integration.

Advances in Osteometric Sorting: Utilizing Diaphyseal CSG Properties for Lower Limb Skeletal Pair-Matching.

Pair-matching of bilateral elements is a major component of resolving commingled remains both in forensic and bioarchaeological contexts. This study presents a new method of osteometric pair-matching of the lower limbs which relies on 3D digital models of the femur and tibia bones. The proposed method, which is accompanied by a freely available open-source implementation, automatically computes a number of osteometric variables including cross-sectional geometric properties from an assemblage of left and right bone antimeres and calculates probabilistically the appropriate matching pairs as well as single elements, whose bones antimere is not present in the given assemblage. The method has been extensively tested on a skeletal sample comprising 396 femurs and 422 tibias from the Athens collection. Our results in testing commingled assemblages with no disparity show that the method's sensitivity is 1 for sorting femurs and 0.997 for sorting tibias, whereas in assemblages with moderate disparity the sensitivity is 0.999 and 0.992 respectively. Our results further indicate that sensitivity is unaffected by the size of the commingled assemblage although the percentage of identified true matching pairs drops as the number of commingled elements increases. This means that all identified antimeres matched to an individual are still very accurately sorted despite not every individual being identified in very large assemblages. The proposed method can facilitate the sorting process of commingled remains both accurately and efficiently, while leaving a very small percentage of unsorted elements that may require further techniques for further individualization.

"What and how should we share?" An inter-method inter-observer comparison of measurement error with landmark-based craniometric datasets.

The present study evaluates the precision and accuracy of photogrammetric 3D modeling of human crania in landmark acquisition and explores the limitations of combining datasets acquired by different observers and different measurement methods. Our working sample comprises 50 adult human crania, which were modeled with 3D photogrammetry. 3D coordinates of 56 landmarks were collected from the 3D models with Meshlab software and an existing corresponding dataset digitized with Microscribe-3DX has been utilized. Measurement error for landmark configurations and Inter Landmarks Distances (ILDs) for each type of landmarks has been assessed through least root mean squared deviation and mean absolute error respectively. Inter-observer error has been assessed on a sub-sample of 20 crania, which was also used for caliper measured ILDs. Between-methods Technical Error Measurement (TEM) based on ILDs has been calculated for evaluating the interchangeability for different datasets. Photogrammetric 3D models and Microscribe-3DX share identical rated accuracy regarding craniometric applications and both methods show increased accuracy in locating type I landmarks as opposed to types II and III. However, photogrammetric 3D models perform better in terms of inter-observer error suggesting higher reliability of measurements. Furthermore, ILDs are less prone to measurement error than landmark configurations. Finally, ILDs exhibit similar relative TEM of about 1.5% between Microscribe, caliper and 3D model based measurement methods. Combining datasets of landmark coordinates acquired from photogrammetric 3D models does not compromise the statistical integrity in terms of measurement error, which also applies to pooling ILD datasets from multiple methods. Nevertheless, compiling 3D datasets from multiple methods for 3DGM analysis should be done cautiously.

A novel method for analyzing long bone diaphyseal cross-sectional geometry. A GNU Octave CSG Toolkit.

The diaphyseal cross-sectional geometric properties of the humerus, femur and tibia have been extensively used for studying their adaptation to mechanical loading. To date common practices for such studies involve either computed tomography or the latex cast method in conjunction with image analysis for calculating such properties. With the advent of modern laser scanning and photogrammetry technologies in biological anthropology, the computation of the cross-sectional geometric properties directly from 3D models is a viable and sensible alternative. Nevertheless, such method has not been properly implemented as yet. A dedicated toolkit, named long-bone-diaphyseal-CSG-Toolkit, comprising a set of functions for the GNU Octave programming language, is presented here. Offering a robust analytical implementation and an easy to follow application either for a single bone or in batch-processing mode, the toolkit requires minimum user intervention and also provides functionality for graphical representation of the calculated periosteal contours and their respective cross-sectional geometric properties. Finally, the long-bone-diaphyseal-CSG-Toolkit utilizes advanced optimization algorithms, which eliminate intra- and inter-observer error by reliably orienting the cross-sectional contours to a well-defined orientation and close to the bone's true anatomical position, which provides a significant advantage over the latex cast method.

Testing the reliability of 3D-ID software in sex and ancestry estimation with a modern Greek sample.

A primary concern in forensic anthropology, when reconstructing the biological profile of an unidentified individual is ancestry and sex estimation. The development of multivariate statistical methods and the assembly of large reference sample databases gave rise to the development of specialized computer software for sex and ancestry estimation. Among various such software, the 3D-ID is the only freely-available program that can handle missing values in the input dataset. The present study evaluates the reliability of 3D-ID in correctly classifying ancestry and sex of 158 test subjects from the Athens Collection, a documented Greek population sample. 3D-ID's classification performance was evaluated both separately and collectively for sex and ancestry. According to our results, the accuracy regarding sex estimation ranged from 74.05% to 86.7% for cases with unknown ancestry and reached 89.87% when testing within the Southeastern European reference group, whereas ancestry estimation accuracy reached 70.9% for correctly classifying the Greek individuals to European population groups. We conclude that 3D-ID software exhibits moderate reliability in ancestry estimation and adequate reliability in sex estimation. The Greek population seems to deviate from the 3D-ID software's reference samples and therefore caution should be taken in interpreting 3D-ID's results of unknown subjects, for which the software's reference sample database may not be representative. 3D-ID's guidelines for using 19-landmark configuration improves the accuracy of ancestry estimation and form variables should be preferred for sexing samples.

An attempt to predict tooth crown height using cementoenamel junction diameters and implications in the quantitative study of dental wear.

SUMMARY: Dental wear has been used extensively in osteoarchaeological studies as a means of exploring dietary patterns and the use of teeth as tools. The present paper aims to test whether crown height can be predicted for premolars and molars based on the mesiodistal and buccolingual diameters of these teeth at the level of the cementoenamel junction (CEJ). Multiple linear regression was used with crown height as dependent variable and diameters at the CEJ as predictors. Our results found that there are cases where the impact of one predictor appears to be statistically significant. However, even in these cases the 95% confidence interval for the predicted value is so broad that makes the accurate determination of the crown height based on the buccolingual or/and mesiodistal diameters at the CEJ impossible.