Darlene A. Weston

Distinct clones of yersinia pestis caused the Black Death

From AD 1347 to AD 1353, the Black Death killed tens of millions of people in Europe, leaving misery and devastation in its wake, with successive epidemics ravaging the continent until the 18th century. The etiology of this disease has remained highly controversial, ranging from claims based on genetics and the historical descriptions of symptoms that it was caused by Yersinia pestis to conclusions that it must have been caused by other pathogens. It has also been disputed whether plague had the same etiology in northern and southern Europe. Here we identified DNA and protein signatures specific for Y. pestis in human skeletons from mass graves in northern, central and southern Europe that were associated archaeologically with the Black Death and subsequent resurgences. We confirm that Y. pestis caused the Black Death and later epidemics on the entire European continent over the course of four centuries. Furthermore, on the basis of 17 single nucleotide polymorphisms plus the absence of a deletion in glpD gene, our aDNA results identified two previously unknown but related clades of Y. pestis associated with distinct medieval mass graves. These findings suggest that plague was imported to Europe on two or more occasions, each following a distinct route. These two clades are ancestral to modern isolates of Y. pestis biovars Orientalis and Medievalis. Our results clarify the etiology of the Black Death and provide a paradigm for a detailed historical reconstruction of the infection routes followed by this disease.

Brief communication: Paleohistopathological analysis of pathology museum specimens: Can periosteal reaction microstructure explain lesion etiology?

The assertion that the microstructure of periosteal new bone formation can be used to differentiate between disease etiologies (Schultz: Yrbk Phys Anthropol 44 2001 106-147; Schultz: Identification of pathological conditions in human skeletal remains, 2nd ed. London: Academic Press 2003 73-109) was tested in a pilot-study, using diagnosed bone specimens from St Georges Hospital Pathology Museum, London, UK. Embedded bone specimens exhibiting pathological periosteal new bone formation were examined using scanning electron microscopy in back-scattered electron imaging mode (SEM-BSE). The results suggest that several histological features (i.e. Grenzstreifen, Polsters, and sinuous lacunae) deemed to be diagnostic of specific pathological conditions are of no specific diagnostic value, as they are encountered in pathological conditions of differing disease etiology. These results tie in with a previous investigation demonstrating a lack of diagnostic qualitative or quantitative characteristics seen in the macroscopic and radiographic appearance of periosteal reactions (Weston: Am J Phys Anthropol 137 2008 48-59).

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.

Estimating body mass from postcranial variables: an evaluation of current equations using a large known-mass sample of modern humans

Many inferences in palaeoanthropology and bioarchaeology rely on estimates of body mass from skeletal material. Body mass estimation is also becoming an area of interest for forensic anthropologists. The most common approach to estimating body mass from the skeleton involves measurements of the postcranium, and a number of equations have been developed for femoral head size and stature plus bi-iliac breadth. These equations have become standard in biological anthropology, but they have rarely been tested on individuals of known mass. In addition, the effects of several assumptions involved in the application of the equations have not been rigorously investigated. Accordingly, this study employed CT scans from a sample of 253 adult modern humans of known body mass to test the accuracy of the most widely used postcranial body mass estimation equations. The results were then used to evaluate several claims concerning the performance of the equations relative to one another. Most of the equations that were tested met the criteria for acceptance as reliable estimators with the male and the combined-sex samples. However, females were not estimated as reliably. In addition, the equations did not always perform consistently or as expected. Overall, our results suggest that estimating body mass with the postcranial equations that are currently available requires more caution than is usually exercised.

Estimating body mass from skeletal material: new predictive equations and methodological insights from analyses of a known-mass sample of humans

Estimating body mass from skeletal material is a key task for many biological anthropologists. As a result, several sets of regression equations have been derived for cranial and postcranial material. The equations have been applied to a wide range of specimens, but several factors suggest they may not be as reliable as generally assumed. Specifically, since many of the equations were derived from small reference samples using proxies for key variables and/or mean data, the nature of the relationship between the skeletal variables and body mass has often not been adequately demonstrated. In addition, few of the equations have been validated on known samples, making their accuracy and precision uncertain. Lastly, because no study has used cranial and postcranial material from the same individuals, the two approaches have never been systematically compared. The present study responded to these issues by deriving new regression equations from cranial and postcranial material using a large sample of modern humans of known-mass and associated skeletal variables measured from CT data. The equations were then tested on an independent sample, also of known mass. The results show that the newly derived equations estimate mass more accurately than existing equations for most variables. However, improvements were modest and accuracy rates remained relatively low. In addition, variables that had previously been argued to be ideal predictors were not the most accurate, and the current criteria used to assess equations did not ensure reliability. Overall, the results suggest that body mass estimates must be used cautiously and that further research is required.

A review of the embryological development and associated developmental abnormalities of the sternum in the light of a rare palaeopathological case of sternal clefting

A sternal cleft or bifid sternum is a rare anterior chest wall abnormality. Although several cases have been reported in clinical literature, very little reference has been made to this anomaly in palaeopathological texts. This paper presents a case of superior sternal clefting observed in a middle-aged female with concurrent Pagets disease and congenital hyperkyphosis excavated from a 19th century Dutch psychiatric asylum cemetery in Bloemendaal, The Netherlands. The embryological development of the sternum and associated developmental abnormalities are reviewed and a differential diagnosis is performed on the suite of observed skeletal anomalies. Goltz syndrome, congenital hypothyroidism, disruption of the Hoxb-4 gene, acute excessive maternal alcohol consumption during pregnancy, Coffin-Lowry syndrome and PHACES syndrome were considered as possible causative agents, with the latter two conditions determined to be the most likely. The psychiatric asylum context, from which the individual came, supports the differential diagnosis as neurological abnormalities are common in these two syndromes. This article demonstrates that the integration of embryology, modern clinical literature and palaeopathological principles is vital in the interpretation of developmental anomalies from an archaeological context.

Estimating fossil hominin body mass from cranial variables: An assessment using CT data from modern humans of known body mass

Body mass estimates are integral to a wide range of inferences in paleoanthropology. Most techniques employ postcranial elements, but predictive equations based on cranial variables have also been developed. Three studies currently provide regression equations for estimating mass from cranial variables, but none of the equations has been tested on samples of known mass. Nor have the equations been compared to each other in terms of performance. Consequently, this study assessed the performance of existing cranial equations using computed tomography scans from a large, documented sample of modern humans of known body mass. Virtual models of the skull were reconstructed and measured using computer software, and the resulting variables were entered into three sets of published regression equations. Estimated and known body masses were then compared. For most equations, prediction errors were high and few individuals were estimated within ±20% of their known mass. Only one equation satisfied the accuracy criteria. In addition, variables that had been previously argued to be good predictors of mass in hominins, including humans, did not estimate mass reliably. These results have important implications for paleoanthropology. In particular, they emphasize the need to develop new equations for estimating fossil hominin body mass from cranial variables.

Life and death at precolumbian Lavoutte, Saint Lucia, Lesser Antilles

Abstract The Caribbean archaeological record requires immediate attention and protection. Development and natural forces have impacted archaeological sites, destroying or severely damaging them. The precolumbian site of Lavoutte, located in northern Saint Lucia, has been known as a major Late Ceramic Age (a.d. 1000–1500) settlement since the 1960s, but it has been damaged over the past decades by both natural and human processes. Multidisciplinary field and laboratory methodologies were implemented during a rescue project at the site from 2009 to 2010. This paper presents the results of collaborative efforts between local and international organizations. The first goal was to demonstrate the importance of protection and rescue of endangered archaeological sites. Secondly, we aimed to show that by adopting a multidisciplinary approach including artifact analysis, bioarchaeology, paleoenvironmental reconstruction, and geochemistry, severely damaged sites can be of significant informational value.

The ancestral shape hypothesis: An evolutionary explanation for the occurrence of intervertebral disc herniation in humans

BackgroundRecent studies suggest there is a relationship between intervertebral disc herniation and vertebral shape. The nature of this relationship is unclear, however. Humans are more commonly afflicted with spinal disease than are non-human primates and one suggested explanation for this is the stress placed on the spine by bipedalism. With this in mind, we carried out a study of human, chimpanzee, and orangutan vertebrae to examine the links between vertebral shape, locomotion, and Schmorl’s nodes, which are bony indicators of vertical intervertebral disc herniation. We tested the hypothesis that vertical disc herniation preferentially affects individuals with vertebrae that are towards the ancestral end of the range of shape variation within Homo sapiens and therefore are less well adapted for bipedalism.ResultsThe study employed geometric morphometric techniques. Two-dimensional landmarks were used to capture the shapes of the superior aspect of the body and posterior elements of the last thoracic and first lumbar vertebrae of chimpanzees, orangutans, and humans with and without Schmorl’s nodes. These data were subjected to multivariate statistical analyses.Canonical Variates Analysis indicated that the last thoracic and first lumbar vertebrae of healthy humans, chimpanzees, and orangutans can be distinguished from each other (p<0.028), but vertebrae of pathological humans and chimpanzees cannot (p>0.4590). The Procrustes distance between pathological humans and chimpanzees was found to be smaller than the one between pathological and healthy humans. This was the case for both vertebrae. Pair-wise MANOVAs of Principal Component scores for both the thoracic and lumbar vertebrae found significant differences between all pairs of taxa (p<0.029), except pathological humans vs chimpanzees (p>0.367). Together, these results suggest that human vertebrae with Schmorl’s nodes are closer in shape to chimpanzee vertebrae than are healthy human vertebrae.ConclusionsThe results support the hypothesis that intervertebral disc herniation preferentially affects individuals with vertebrae that are towards the ancestral end of the range of shape variation within H. sapiens and therefore are less well adapted for bipedalism. This finding not only has clinical implications but also illustrates the benefits of bringing the tools of evolutionary biology to bear on problems in medicine and public health.

Principal component analysis in the evaluation of osteoarthritis

OBJECTIVES The purpose of this study is to demonstrate advantages of principal component analysis (PCA) as a standardized procedure in the evaluation of osteoarthritis (OA) in a skeletal series to: (1) compute aggregate scores for joint complexes that accurately capture pathological expression, (2) reveal which variables describe the most sample variation in OA, (3) enable inter- and intra-sample comparison of results, and (4) formulate predictive models from component-based arthritic scores. MATERIALS AND METHODS The sample (144 males, 145 females) is drawn from a large skeletal cemetery collection of modern Europeans of known sex, age, and occupation. OA data was collected using standard ranked categorical scoring. PCA was conducted separately on lumbar spine, pelvis, and knee regions to generate composite OA scores from eigenequations of the first and second principal components (PC). RESULTS Results demonstrate that as severity in OA increases, so does the distribution of OA within the joint surface. In each region, PCA produced the same general pattern with eburnation scoring driving significant changes in composite OA scores, representing earlier to later stages of cartilage degeneration. The distribution of arthritic traits determined by PCA produced an OA score that quantifies the expression of joint changes in varied biological joint structures from most moveable to least mobile, the final stage being joint fusion. OA scores are most highly variable in the lumbar region for both males and females, as compared to the pelvis and knee. CONCLUSIONS PCA is a simple, non-parametric method of extracting relevant information from complex OA datasets and summarizes variation based on correlated multi-attributes to reveal a simplified structure of OA expression. Multivariate techniques like PCA should be used to describe discrete OA samples, and are useful to compute population-specific representative measurements for idiopathic joint OA in a skeletal sample.