Ancient Skeletons Research Articles

Genetic sexing of subadult skeletal remains

When subadult skeletons need to be identified, biological sex diagnosis is one of the first steps in the identification process. Sex assessment of subadults using morphological features is unreliable, and molecular genetic methods were applied in this study. Eighty-three ancient skeletons were used as models for poorly preserved DNA. Three sex-informative markers on the Y and X chromosome were used for sex identification: a qPCR test using the PowerQuant Y target included in PowerQuant System (Promega), the amelogenin test included in ESI 17 Fast STR kit (Promega), and a Y-STR amplification test using the PowerPlex Y-23 kit (Promega). Sex was successfully determined in all but five skeletons. Successful PowerQuant Y-target, Y-amelogenin, and Y-chromosomal STR amplifications proved the presence of male DNA in 35 skeletons, and in 43 subadults female sex was established. No match was found between the genetic profiles of subadult skeletons, and the elimination database and negative control samples produced no profiles, indicating no contamination issue. Our study shows that genetic sex identification is a very successful approach for biological sexing of subadult skeletons whose sex cannot be assessed by anthropological methods. The results of this study are applicable for badly preserved subadult skeletons from routine forensic casework.

Osteoarthritis.

The clinical appearance and radiological pattern of osteoarthritis have been identified in the skeletons of dinosaurs some 50-70 million years old, and in Egyptian mummies, and in ancient skeletons in England. Osteoarthritis patterns of joint involvement, often referred to as primary osteoarthritis, can be seen in the hands, spinal facet joints, hips, knees and feet, but can also be termed secondary osteoarthritis when seen in any joint that has had trauma, sepsis, surgery or metabolic insult. The prevalence of osteoarthritis increases with age. The histology and pathophysiology both demonstrate an inflammatory process. While there have been studies of genetic predisposition, the basic cause of primary osteoarthritis has not been determined.

Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology.

In forensic kinship analysis and human identification cases, analysis of STRs is the gold standard. When badly preserved ancient DNA is used for kinship analysis, short identity SNPs are more promising for successful amplification. In this work, kinship analysis was performed on two skeletons from the Early Middle Ages. The surface contaminants of petrous bones were removed by chemical cleaning and UV irradiation; DNA was isolated through full demineralization and purified in an EZ1 Advanced XL machine. The PowerQuant kit was used to analyze DNA yield and degradation, and on average, 17 ng DNA/g of petrous bone was obtained. Both skeletons were typed in duplicate for STR markers using the Investigator EssplexPlus SE QS kit, and comparison of partial consensus genotypes showed shared allelic variants at most loci amplified, indicating close kinship. After statistical calculation, the full-sibling kinship probability was too low for kinship confirmation, and additional analyses were performed with PCR-MPS using the Precision ID Identity Panel. The HID Ion Chef Instrument was used to prepare the libraries and for templating and the Ion GeneStudio S5 System for sequencing. Analysis of identity SNPs produced full genetic profiles from both skeletons. For combined likelihood ratio (LR) calculation, the product rule was used, combining LR for STRs and LR for SNPs, and a combined LR of 3.3 × 107 (corresponding to a full-sibling probability of 99.999997%) was calculated. Through the SNP PCR-MPS that followed the STR analysis, full-sibling kinship between the ancient skeletons excavated from an early medieval grave was confirmed.

Comparison of DNA preservation between adult and non-adult ancient skeletons.

Studies evaluating DNA preservation in non-adults, or comparing preservation in adults and non-adults, are very rare. This study compares the preservation of DNA in the skeletal remains of adults and non-adults. It compares the quality and quantity of DNA recovered from different skeletal elements of adults and non-adults, and from non-adults of different age classes. In addition, the preservation of DNA in males and females is compared. Bone DNA preservation was estimated by measuring nuclear DNA concentration and its degradation, and through STR typing success. The study analyzed 29 adult skeletons and 23 non-adult skeletons from the Ljubljana-Polje archeological site, dating from the seventeenth to nineteenth century, and up to four skeletal elements (petrous bone, femur, calcaneus, and talus) were included. After full demineralization extraction, the PowerQuant System and the PowerPlex ESI 17 Fast System (Promega) were used for qPCR and STR typing, respectively. The results showed that, among the four bone types analyzed, only the petrous bone proved to be a suitable source of DNA for STR typing of non-adult skeletal remains, and DNA yield is even higher than in the adult petrous bone, which can be attributed to the higher DNA degradation observed in the adult petrous bone. In adult skeletons, petrous bones and tali produced high STR amplification success and low DNA yield was observed in adult femurs. The results of this study are applicable for the sampling strategy in routine forensic genetics cases for solving identification cases, including badly preserved non-adult and also adult skeletons.

Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach.

To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools.

An Ancient Mesiodens Investigated by Cone Beam CT

This article presents the complex case study of an ancient skeleton presenting a maxillary supernumerary tooth (mesiodens). The skeleton was found in an archaeological site in the western part of Romania and was dated back to the Eneolithic period, some 5500 years ago. The aim of this article is to analyze the mesiodens and the jaws in light of current knowledge regarding anomalies of dental development of past and present-time populations. The cranial remains were investigated from an orthodontic perspective through inspection and cone beam computed tomography (CBCT) scan. The occlusion was analyzed according to Angle’s classification and observations were made regarding the presence of calculus, dental wear, presence of caries, bone loss and ante-mortem tooth loss. Observations were made regarding tooth dimensions and comparisons were made with modern population. In this specific case, the mesiodens caused minimum disruption within the upper dental arch and the occlusion. Additionally, it did not have any negative impact on the adjacent teeth or cause any other complication. Judging by the analysis of the jaws, the presence of the mesiodens had little impact on the overall oral health of the person. As suggested by other findings in the scientific literature, the mesiodens is an anomaly found throughout all historical periods, from the oldest archaeological sites to present day.

Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT.

Ancient dental calculus, formed from dental plaque, is a rich source of ancient DNA and can provide information regarding the food and oral microbiology at that time. Genomic analysis of dental calculus from Neanderthals has revealed the difference in bacterial composition of oral microbiome between Neanderthals and modern humans. There are few reports investigating whether the pathogenic bacteria of periodontitis, a polymicrobial disease induced in response to the accumulation of dental plaque, were different between ancient and modern humans. This study aimed to compare the bacterial composition of the oral microbiome in ancient and modern human samples and to investigate whether lifestyle differences depending on the era have altered the bacterial composition of the oral microbiome and the causative bacteria of periodontitis. Additionally, we introduce a novel diagnostic approach for periodontitis in ancient skeletons using micro-computed tomography. Ancient 16S rDNA sequences were obtained from 12 samples at the Unko-in site (18th-19th century) of the Edo era (1603–1867), a characteristic period in Japan when immigrants were not accepted. Furthermore, modern 16S rDNA data from 53 samples were obtained from a database to compare the modern and ancient microbiome. The microbial co-occurrence network was analyzed based on 16S rDNA read abundance. Eubacterium species, Mollicutes species, and Treponema socranskii were the core species in the Edo co-occurrence network. The co-occurrence relationship between Actinomyces oricola and Eggerthella lenta appeared to have played a key role in causing periodontitis in the Edo era. However, Porphyromonas gingivalis, Fusobacterium nucleatum subsp. vincentii, and Prevotella pleuritidis were the core and highly abundant species in the co-occurrence network of modern samples. These results suggest the possibility of differences in the pathogens causing periodontitis during different eras in history.

The elusive parasite: comparing macroscopic, immunological, and genomic approaches to identifying malaria in human skeletal remains from Sayala, Egypt (third to sixth centuries AD)

Although malaria is one of the oldest and most widely distributed diseases affecting humans, identifying and characterizing its presence in ancient human remains continue to challenge researchers. We attempted to establish a reliable approach to detecting malaria in human skeletons using multiple avenues of analysis: macroscopic observations, rapid diagnostic tests, and shotgun-capture sequencing techniques, to identify pathological changes, Plasmodium antigens, and Plasmodium DNA, respectively. Bone and tooth samples from ten individuals who displayed skeletal lesions associated with anaemia, from a site in southern Egypt (third to sixth centuries AD), were selected. Plasmodium antigens were detected in five of the ten bone samples, and traces of Plasmodium aDNA were detected in six of the twenty bone and tooth samples. There was relatively good synchronicity between the biomolecular findings, despite not being able to authenticate the results. This study highlights the complexity and limitations in the conclusive identification of the Plasmodium parasite in ancient human skeletons. Limitations regarding antigen and aDNA preservation and the importance of sample selection are at the forefront of the search for malaria in the past. We confirm that, currently, palaeopathological changes such as cribra orbitalia are not enough to be certain of the presence of malaria. While biomolecular methods are likely the best chance for conclusive identification, we were unable to obtain results which correspond to the current authentication criteria of biomolecules. This study represents an important contribution in the refinement of biomolecular techniques used; also, it raises new insight regarding the consistency of combining several approaches in the identification of malaria in past populations.

The Song of the Science Mermaid: A Philosophical Trilogue on the Osteological Paradox

As a modern academic Ulysses, the historical scientist is enticed by numerous plausible scientific theories that can explain the historical data in search of the truth. However, the predicament of her work is to inevitably crash onto the rocks and cliffs of uncertainty. The problem discussed in this paper is that several scientific models can be suitable to account for the same empirical observations. The risk of falling into speculation is looming, and exceedingly dangerous in science. This is also the case in archaeological sciences, such as bioarchaeology. A bioarchaeologist frequently encounters traces of disease in ancient skeletons, and pertinent patterns may often result from equally probable different causes. This is a methodological issue commonly encountered in the interpretation of pathological patterns in human remains, and constitutes part of the problem known in bioarchaeology as the osteological paradox. During an informal trilogue, three characters discuss the osteological paradox, and attempt to define it in philosophical terms. The aim of this work is to present the problems of scientists with the philosophical approach to the debate between scientific realism and antirealism, focusing in particular on the so-called problem of underdetermination. Our original approach is to apply the distinction between ‘how-possibly’ models and ‘how-actually’ models by Alisa Bokulich to archaeological issues, integrating various fields of science with a multidisciplinary and omnivorous approach. The trilogue ends providing the historical scientist with reasons and means to believe in her ability to conceive of true and reliable scientific models to interpret the historical past.

Trauma in Ancient Skeletons: Case reports from Minnetpınarı and Güllüdere Materials

Amaç: İnsan iskeletlerinde görülen travma bulgularının tanımlanması kişilerin günlük yaşamlarında, ölüm zamanı veya sonrasında başlarından geçen travmatik olaylar hakkında bilgi edinmek açısından önemlidir. Bu çalışmanın amacı, Minnetpınarı ve Güllüdere arkeolojik kazılarında bulunan antik dönem insan iskeletlerindeki travmaları belirlemek, bu patolojik durumlara neden olan mekanizmaları anlamak adına adli antropolojik incelemelerdeki travma özellikleri ile karşılaştırmak ve antik dönemde yaşamış bu iki insan topluluğunun yaşam koşulları ve sağlık durumları hakkında yapılmış çalışmalara katkıda bulunmaktır.Yöntem: 60 bireye ait kemikler makroskobik olarak incelendi. Çok parçalı kemikler sıcak silikonla rekonstrüksiyon yapılarak bütünlendi. Travma çeşitleri ve kırık morfolojileri tanımlandı. Tüm bulgular fotoğraflanarak belgelendi. Bulgular: 4 bireyde antemortem travma bulgusu, tüm bireylerde çok sayıda postmortem kırıklar ve Güllüdere kafataslarında plastik deformasyonlar görüldü. Antemortem travmaların alt ve üst ekstremitelerde mevcut olduğu ve yüksek olasılıkla künt travma sonucunda meydana geldikleri izlendi. Sonuç: Antik iskeletlerdeki antemortem travma bulgularının, adli antropolojik örneklerdeki bulgularla aynı patolojik özelliklere sahip olduğu görüldü. Antik iskelet materyali üzerinde travma tespiti ve yorumlamasının mümkün olduğu ve kırıkların iyileşme özelliklerinin bireylerin sağlık durumları hakkında bilgi sağladığı görüldü. Güllüdere kafataslarında izlenen plastik deformasyonun postmortem süreçte, kemiğin kolajen yapısını kaybetmediği zaman içerisinde, muhtemelen mezar dolgularından veya zaman içerisinde meydana gelen mezar çökmelerinden kaynaklanan basınçtan ötürü gerçeklemiş olabileceği sonucuna varıldı.

Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus.

We have recently developed bioinformatic tools to accurately assign metagenomic sequence reads to microbial taxa: SPARSE for probabilistic, taxonomic classification of sequence reads; EToKi for assembling and polishing genomes from short-read sequences; and GrapeTree, a graphic visualizer of genetic distances between large numbers of genomes. Together, these methods support comparative analyses of genomes from ancient skeletons and modern humans. Here, we illustrate these capabilities with 784 samples from historical dental calculus, modern saliva and modern dental plaque. The analyses revealed 1591 microbial species within the oral microbiome. We anticipated that the oral complexes of Socransky et al., which were defined in 1998, would predominate among taxa whose frequencies differed by source. However, although some species discriminated between sources, we could not confirm the existence of the complexes. The results also illustrate further functionality of our pipelines with two species that are associated with dental caries, Streptococcus mutans and Streptococcus sobrinus. They were rare in historical dental calculus but common in modern plaque, and even more common in saliva. Reconstructed draft genomes of these two species from metagenomic samples in which they were abundant were combined with modern public genomes to provide a detailed overview of their core genomic diversity.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

THE VIEW ON THE DENTAL MORBIDITY INDICATORS OF THE CHILDREN UKRAINIAN NOGAI POPULATION AT THE XV CENTURY DEALS WITH THE NEW STUDYING METHODS USED FOR ANTHROPOLOGICAL MATERIAL FROM THE MAMAY GORA BURIAL GROUND

The subject matter was the children dental status having involved in study anthropological bone material different historical eras. The 133 remains skeletons of children were examined. The control and main groups consisted with the skeletons of children who had lived in the Nogai and Golden Horde periods, respectively, which in turn the last included children skeletons of earlier historical times.
 The author’s method was used in our scientific research. The ancient people skeletons were examined in historical and medical anthropology laboratory of the municipal institution “Conservation Centre and Research of Archaeological Monuments” of the Poltava Regional Council and the Department of Pediatric Therapeutic Dentistry with the Dental Diseases Prevention UMSA.
 The control group has included the children with maxillofacial pathology but their musculoskeletal system hasn’t been changed. However, two children have a “thin line” dental deposit in permanent and primary teeth.
 Two enamel hypoplasia specimens were detected in bone materials, five specimens of anomalies development dento-maxillofacial region and two dental specimens with markers determined of social society affiliation in the main children's group of the Middle Ages consist with of Golden Horde children. The main group results were compared with control group related to one period.
 The increase in the incidence of dental pathology was directly proportional to the number of children examined in the group.
 The dental pathology incidence was directly proportional relation increases to the examined children quantity in the group. The bone skeleton injury was found only in Golden Horde children group. The Middle Ages is characterized with the average diseases prevalence in Europe and America populations.
 We were determined the carious process and periodontal pathology were absence in deciduous and permanent teeth in the base and control children groups represent Middle Ages, after morphological and statistical processing of the collected archaeological, bone material.
 The dental mineralized deposits have a similar shape in base and control groups children of the Middle Ages in the studied territory of Ukraine.
 The dental mineralized plaque had a huge volume and was occupied a massive teeth square in examined children group identified with earlier historical periods and the Middle Ages. The research has shown that the dental deposit has a gradual evolutionary development in teeth of children groups at the Middle Ages.

Pseudopathological vertebral changes in a young individual from Herculaneum (79 C.E.).

Post mortem abnormal modification of bone are known as pseudopathologies. The geochemical characteristic of the burial soil and/or the presence of biological agents may produce marked changes in bone preservation. This could be the case for a young individual, E74, from Herculaneum, which was a Roman town near Naples completely destroyed by the volcanic eruption of Mt. Vesuvius in 79 CE. E74 is an incomplete skeleton of a male individual of 7-8 years of age. Its second and third cervical vertebrae, the eighth thoracic vertebra and the first lumbar vertebra show a septum dividing the vertebral foramen. This condition could be diagnosed as diastematomyelia that consists of the splitting of the spinal cord or cauda equina. In particular Type I malformations consist of two hemicords separated into two dural tubes by a bone septum. The gross anatomy and histological aspects of the vertebrae and their septa were investigated through macroscopic, microscopic, radiographic and chemical analyses. The results demonstrate that the vertebral septum is constituted by three layers of inorganic substances deposited at different times on a thin, probably organic, substrate (original meninges?). The central layer contain framboidal pyrite, that is a sedimentary mineral rarely found in ancient human skeletons. The septum splitting the vertebral canal of individual E74 is consequent to a taphonomic event and is not due to a pathological condition. Distinguishing between ante and post mortem alterations can be a challenging exercise even for the experienced paleopathologists and, as this case indicates, paleopathological diagnoses should be supported by detailed examinations.

The repatriation of the Palaeoamericans: Kennewick Man/the Ancient One and the end of a non-Indian ancient North America

AbstractThis article considers the repatriation of some the most ancient human skeletal remains from the United States as two sorts of ending: their end as objects of scientific study, and their end as ancient non-American Indian settlers of North America. In the 1990s, some prominent physical anthropologists and archaeologists began replacing ‘Palaeoindian’ with the new category of ‘Palaeoamerican’ to characterize the western hemisphere's earliest inhabitants. Kennewick Man/the Ancient One, a nearly nine-thousand-year-old skeleton, convinced some anthropologists that contemporary Native American people (descendants of Palaeoindians) were not biologically related to the very first American colonists. The concept of the Palaeoamerican therefore denied Native American people their long-held status as the original inhabitants of the Americas. New genetic results, however, have contradicted the craniometric interpretations that led to these perceptions, placing the most ancient American skeletons firmly back in the American Indian family tree. This article describes the story of Kennewick Man/the Ancient One, the most famous ‘Palaeoamerican’; explores how repatriation has been a common end for many North American collections (Palaeoindians included); and enumerates what kind of ending repatriation may represent materially and ethically for anthropological science.

Ancient pelvis reconstruction from collapsed component bones using statistical shape models

We propose a new method for recovering the pelvis of an ancient skeleton from its three component bones with collapsed surfaces. The proposed method uses four types of statistical shape models (SSMs) for the bones. The SSM for each bone describes the mean shape and shape variations of a class of bones. The SSMs for the three component bones are employed to restore the shapes of the component bones. The SSM for the whole pelvis provides the natural anatomical shape of the pelvis and the spatial relationship among the sacrum and the hip bones. Therefore, the three component bones are aligned by using the SSM for the pelvis. The experimental results show that our method achieves reliable reconstruction of the ancient pelvis shape despite having collapsed surfaces in its component bones.

An Ancient Skeleton with Multiple Osteoblastic Bone Lesions Containing a Scapular Sunburst Appearance from a 5th-6th Century Grave Excavated in Oita, Japan.

A human skeleton of a middle-aged adult male was found in a 5th–6th century Kinoue-Kodo stone coffin excavated from the southwest marginal region of the Oita plains, northeast Kyushu, Japan. The skeleton was buried respectfully in the ancient tomb, and red pigment was applied to his face after death. We report herein findings from computed tomography imaging of the skeleton and discuss the multiple osteoblastic lesions identified in the humerus, scapula, clavicle, vertebra, pelvic bones, and skull of this individual. These lesions comprised cortical bone thickening with periosteal reaction localized to the surface and osteosclerotic changes mainly observed in the trabecular structure of cancellous bone. In particular, a typical sunburst pattern was also noted on the left scapula as another characteristic lesion found in this case. By differential diagnosis, the disease suffered by this individual was most likely to be metastatic bone tumors, especially of prostate cancer. This person may have survived until many bone metastases had developed throughout his whole body.

Ancient deer skeleton may reveal how Neanderthals hunted prey

Ancient deer skeleton may reveal how Neanderthals hunted prey

This ancient skeleton suggests humans were riding donkeys nearly 5000 years ago

This ancient skeleton suggests humans were riding donkeys nearly 5000 years ago

Ancient pathogen DNA in human teeth and petrous bones.

Recent ancient DNA (aDNA) studies of human pathogens have provided invaluable insights into their evolutionary history and prevalence in space and time. Most of these studies were based on DNA extracted from teeth or postcranial bones. In contrast, no pathogen DNA has been reported from the petrous bone which has become the most desired skeletal element in ancient DNA research due to its high endogenous DNA content. To compare the potential for pathogenic aDNA retrieval from teeth and petrous bones, we sampled these elements from five ancient skeletons, previously shown to be carrying Yersinia pestis. Based on shotgun sequencing data, four of these five plague victims showed clearly detectable levels of Y. pestis DNA in the teeth, whereas all the petrous bones failed to produce Y. pestis DNA above baseline levels. A broader comparative metagenomic analysis of teeth and petrous bones from 10 historical skeletons corroborated these results, showing a much higher microbial diversity in teeth than petrous bones, including pathogenic and oral microbial taxa. Our results imply that although petrous bones are highly valuable for ancient genomic analyses as an excellent source of endogenous DNA, the metagenomic potential of these dense skeletal elements is highly limited. This trade‐off must be considered when designing the sampling strategy for an aDNA project.

Thirty‐Four Years of Stable Isotopic Analyses of Ancient Skeletons in China: an Overview, Progress and Prospects

AbstractStable isotope analysis of ancient skeletons has become a routine method and widely used to answer diverse archaeological questions related to the human (animal) diets since the initial study in 1977. However, this study in china is underestimated and much less unknown to international circles considering the infrequent publications in English journals. In this review paper, the research history in China was overviewed shortly and then, the research progresses concerning different research themes, such as the chronological trajectory of human diets, the development and spread of agriculture, the mechanism of animal domestication, human social hierarchy, and so on, were introduced in detail, trying to draw a rough framework of human dietary evolution given the unique Chinese geography and cultures. At last, the potential research directions were also suggested for the future studies.