Statistical methods for bioarchaeology: applications of age-adjustment and logistic regression to comparisons of skeletal populations with differing age-structures

Previous studies of patterns of osteoarthritis involvement in prehistoric skeletal populations have been used to suggest differences in lifestyle or subsistence patterns. In spite of the intriguing nature of such studies, inadequate controls for the potential confounding effects of age have made results less secure than they appear. While researchers remain unable to control for the inherent limitations imposed by preservation bias, meaningful advancement could be made in the analysis of these data. Here we propose two methods from epidemiology that would allow more robust comparisons between populations with differing age-structures: age-adjustment and logistic regression. We apply these two methods to previously published data from prehistoric populations of the American Great Basin. In doing so, we are able to discern sex differences in risk for osteoarthritis at the shoulder (beta = −1.82, SE = 0.74, OR = 0.16, 95% CI = 0.04–0.69, p = 0.013), elbow (beta = −2.07, SE = 0.82, OR = 0.13, 95% CI = 0.03–0.63, p = 0.011), and in the foot (beta = −3.11, SE = 1.57, OR = 0.04, 95% CI = 0.00–0.97, p = 0.048), that were not noted in previous analyses of these data. These findings suggest that greater clarity of results and more precise comparisons of risk may be achieved by using these methods. We conclude that further application of these methods to bioarchaeological studies would potentially improve what can be said about prehistoric health patterns and lifeways.     

Two cases of leprosy from Žatec (Bohemia), dated to the turn of the 12th century and confirmed by DNA analysis for Mycobacterium leprae

The leprosy known today primarily from tropical areas was a relatively common disease in European Middle Ages. This article describes two skeletons bearing palaeopathological indications of leprosy from a cemetery at ?atec in North-West Bohemia (Czech Republic). The archaeological context clearly shows that these individuals were buried prior to the second decade of the 12th century, and most probably in the second half of 11th century. This rules out the possibility that these individuals might have contracted the disease in connection with the Crusades, in which a Bohemian contingent under Prince Vladislav II participated from 1141 to 1142. Molecular genetic methods were applied to detect specific DNA fragments of the causative agent of leprosy, Mycobacterium leprae. The nasal concha of one individual yielded DNA that could be directly sequenced after isolation and amplification. The vertebral body of the second individual, on the other hand, did not provide DNA of sufficient quality for direct sequencing and only weak amplification was detectable. The morphological and genetic analyses both indicate that leprosy existed prior to the Crusades in medieval Bohemia, albeit that its prevalence was probably not as great as in northern or western Europe.     

Analysis of ancient mycolic acids by using MALDI TOF MS: response to “Essentials in the use of mycolic acid biomarkers for tuberculosis detection” by Minnikin et al., 2010

The mycobacterial cell wall is consists of several long chain lipid and glycolipid components. Mycolic acids are major and unique fraction of the cell envelope of mycobacteria that include the ancient causative agents of tuberculosis and leprosy. The analytical investigation of these lipid biomarker residues is one of the most promising perspectives in the field of molecular paleopathology. Recently published in this journal, Minnikin et al. present a systematic critique of the MALDI TOF MS analysis for determination of ancient mycolic acids, focusing on our previous paper. In this study, our mass spectrometric investigations by commonly used 2,5 DHB matrix were presented with our comments to the critique authors. On the base of our previous and recent mass spectrometric results we have to realize that the clinical protocols and standards cannot directly be used for the biomolecular paleopathological investigations. The applicability of the recent mycobacterial and clinical results is very limited in the biomolecular archaeology, thus the recent scientific results and protocols should be adapted carefully to bioarchaeological sciences.     

Health Patterns of the Etruscan Population (6th–3rd Centuries bc) in Northern Italy: The Case of Spina

A sample of 303 skeletons from the Etruscan necropolis of Spina (Ferrara, Italy, 6th–3rd centuries bc ) was examined for paleopathological lesions in order to assess the general health, diseases and quality of life of this Iron Age population. The observed pathologies included porotic hyperostosis, specific and aspecific infections, metabolic and endocrine disorders, tumours and osteoarthritis. A total of 46.7% of adults and 7.7% of subadults showed at least one pathological lesion. Statistical comparisons were made between sexes and adult‐age classes (20–35 years and >35 years) to analyse the prevalence of the lesions. The analysis of porotic hyperostosis and osteoperiostitis allowed to determine the general health status of this group, and the analysis of osteoarthritis allowed to hypothesise a gender division of labour. The results suggest a relatively high‐life expectancy for the time as well as good health and quality of life. The few specific infections and metabolic disorders indicate fairly good nutrition, while the high frequency of porotic hyperostosis can be partly linked to some type of hereditary anaemia. Copyright © 2015 John Wiley & Sons, Ltd.     

Essentials in the use of mycolic acid biomarkers for tuberculosis detection: response to “High-throughput mass spectrometric analysis of 1400-year-old mycolic acids as biomarkers for ancient tuberculosis infection” by

High molecular weight long-chain mycolic acids are key structural components of the cell envelope of Mycobacterium tuberculosis and they are established as biomarkers for the identification of both ancient and modern tuberculosis. Mycolic acids from M. tuberculosis have a characteristic profile, reflecting contributions from five major distinct homologous series of mycolate structural types. Diagnosis of tuberculosis in archaeological material, using mycolic acid biomarkers, depends on objective recognition of the key characteristic mycolic acid components. A recent article in this journal claimed that tuberculosis could be confirmed in ancient bones by high throughput mass spectrometric analysis of mycolic acids. Scrutiny of the data presented reveals no convincing evidence for the presence of mycolic acids, characteristic of the M. tuberculosis complex, in the skeletal remains examined. This communication reviews the essential criteria necessary for positive tuberculosis diagnosis, using mycolic acids.     

Deficiencies and challenges in the study of ancient tuberculosis DNA

We explore the standards of research and reporting needed to justify the destructive analysis of archaeological human bone for biomolecular studies of ancient tuberculosis (TB). Acceptable standards in osteological interpretation have been met in some biomolecular papers, but there are also cases where insufficient care has been taken in distinguishing between pathognomonic lesions and those that are ‘consistent with’ a diagnosis of TB. Some biomolecular studies have failed to recognize that archaeological bones might be contaminated with environmental mycobacteria whose DNA could give rise to false positives in polymerase chain reactions directed at members of the Mycobacterium tuberculosis complex. The difficulties of applying spoligotyping to ancient DNA have also been underestimated and conclusions drawn from such analyses are often weakly supported. Assumptions that mycobacterial DNA preserves better than human DNA, and that contamination with modern DNA is less of a problem, has led in some cases to a laxity in research standards with insufficient attention paid to the need to authenticate ancient DNA results. We illustrate our concerns by reference to a recent paper reporting biomolecular detection of ancient TB DNA in skeletons from the eastern Mediterranean Neolithic settlement of Atlit-Yam. We are unconvinced that the skeletal evidence presented in this paper gives sufficient indication of TB to warrant destructive analysis, and we are concerned that during the biomolecular part of the project inadequate attention was paid to the possibility that results might be due to laboratory cross-contamination or to amplification of environmental mycobacterial DNA present in the bones.     

Consequences of conquest? The analysis and interpretation of subadult trauma at Puruchuco-Huaquerones, Peru

This paper examines bioarchaeological evidence of violence and traumatic injury on subadult skeletal remains from two Late Horizon (A.D. 1470-1540) cemeteries within the archaeological zone of Puruchuco-Huaquerones, Peru. Here we present the frequency and types of traumatic lesions on the 242 subadults analyzed. We observed significant increases in the frequency of subadult trauma, particularly among the burials associated with Spanish Conquest. Specifically, we noted a statistically significant increase in the frequency of cranial trauma in a subsample of individuals from one of two cemeteries at the site, 57AS03. These perimortem cranial injuries suggest an intensification of violence and lethality that may have affected the children from this community. We then discuss the biocultural implications of this analysis within the context of Spanish invasion and conquest.     

Paleopathology of The Population of Krasnoyarsk,Central Siberia (Pokrovskiy and Voskresensko-Preobrazhenskiy Cemeteries of the 17th– Early 20th Centuries)

Published data on the paleopathology of Siberian populations are scarce. However, two samples of adult and non- adult skeletons taken from excavations at the Pokrovskiy (17th–18th centuries) and Voskresensko-Preobrazhenskiy (17th–early 20th century) cemeteries in Krasnoyarsk (123 and 204; 101 and 81, respectively) revealed cases of rickets, tuberculosis, and congenital syphilis in children, and vertebral tuberculosis and tertiary syphilis in adults. Trauma areas included ribs, hands, forearms, and tibiae. These two samples provide evidence on which to base an assessment of the health of the Krasnoyarsk population from 1628 to the early 1900s.     

Identification of urate crystals in gouty individuals

In paleopathology cases of gout have traditionally been identified using the character of erosive bony lesions, but in clinical medicine identification of monosodium urate crystals in joint fluid plays a central role in diagnosis. Work undertaken on three skeletal individuals who had been buried, demonstrates that crystals can be identified using polarising microscopy. The crystals were identified as monosodium urate. Results from this study appear to demonstrate that identification of monosodium urate crystals could be used to assist in the diagnosis of gout in paleopathology. Further work is required to establish the full range of spatial and temporal contexts from which such crystals might be found.