3D shape analyses of extant primate and fossil hominin vertebrae support the ancestral shape hypothesis for intervertebral disc herniation

BACKGROUND

Recently we proposed an evolutionary explanation for a spinal pathology that afflicts many people, intervertebral disc herniation (Plomp et al. [2015] BMC Evolutionary Biology 15, 68). Using 2D data, we found that the bodies and pedicles of lower vertebrae of pathological humans were more similar in shape to those of chimpanzees than were those of healthy humans. Based on this, we hypothesized that some individuals are more prone to intervertebral disc herniation because their vertebrae exhibit ancestral traits and therefore are less well adapted for the stresses associated with bipedalism. Here, we report a study in which we tested this "Ancestral Shape Hypothesis" with 3D data from the last two thoracic and first lumbar vertebrae of pathological Homo sapiens, healthy H. sapiens, Pan troglodytes, and several extinct hominins.

RESULTS

We found that the pathological and healthy H. sapiens vertebrae differed significantly in shape, and that the pathological H. sapiens vertebrae were closer in shape to the P. troglodytes vertebrae than were the healthy H. sapiens vertebrae. Additionally, we found that the pathological human vertebrae were generally more similar in shape to the vertebrae of the extinct hominins than were the healthy H. sapiens vertebrae. These results are consistent with the predictions of the Ancestral Shape Hypothesis. Several vertebral traits were associated with disc herniation, including a vertebral body that is both more circular and more ventrally wedged, relatively short pedicles and laminae, relatively long, more cranio-laterally projecting transverse processes, and relatively long, cranially-oriented spinous processes. We found that there are biomechanical and comparative anatomical reasons for suspecting that all of these traits are capable of predisposing individuals to intervertebral disc herniation.

CONCLUSIONS

The results of the present study add weight to the hypothesis that intervertebral disc herniation in H. sapiens is connected with vertebral shape. Specifically, they suggest that individuals whose vertebrae are towards the ancestral end of the range of shape variation within H. sapiens have a greater propensity to develop the condition than other individuals. More generally, the study shows that evolutionary thinking has the potential to shed new light on human skeletal pathologies.

Testing landmark redundancy for sex-based shape analysis of the adult human os coxa

OBJECTIVES

To test the individual effectiveness of common landmarks used in sex estimation of whole adult coxal bones in sex-based shape analysis and propose a method to determine how many principal components of sex-based shape to include for discriminant function analysis.

METHODS

Three-dimensional models (NextEngine desktop laser scanner) of left and right os coxae from 396 individuals (William Bass Skeletal Collection, Forensic Anthropology Centre, University of Tennessee, Knoxville, TN) were subjected to shape analysis using 32 landmarks (Landmark 3.6, Institute for Data Analysis and Visualization). Each landmark was individually removed and subjected to a new principal component analysis to identify the effect omitting a landmark has on PC1/PC2 ordination. Landmarks that poorly discriminated sex-based shape were considered redundant for analysis on sex estimation.

RESULTS

This study identified 17 landmarks that represent sex-based shape of right and left coxal bones most effectively, these are: the anterior superior iliac spine; posterior superior iliac spine; posterior inferior iliac spine; iliac crest; apex of the auricular surface; greater sciatic notch; ischial spine; superior, inferior and distal points on ischial tuberosity; superior, inferior and midpoint on the symphyseal face; arcuate eminence; ischiopubic ramus; posterosuperior and anterosuperior points on the acetabular rim. The first and second PCs of the 17-landmark configuration correctly predicted sex in 98.5% of cases; better than a 32-landmark configuration (96%) and better than previous landmark studies on whole coxal bone sex-based shape.

CONCLUSIONS

These 17 landmarks represent more meaningful data for sex-based shape analysis in PC1 and 2 and concentrate meaningful sex-based shape data to the first five PCs that make up over 50% of the total shape variance.

The relationship of age, activity, and body size on osteoarthritis in weight-bearing skeletal regions

This study examined the simultaneous impact of multiple underlying factors on OA expression in weight-bearing joints of the vertebrae and lower limb of a modern European skeletal sample (Lisbon and Sassari). OA was evaluated using standard ranked categorical scoring; composite OA scores derived through principal component analysis. Body size was calculated from postcranial measurements; torsional strength (J) of the femoral midshaft was calculated from three-dimensional surface models, size standardized and used as a proxy for activity. A standard multiple regression was applied. In all regions, the linear combination of age, body mass, stature, and J was significantly related to differences in OA. Across all joints, age was the strongest predictor; neither body size, nor activity variables demonstrated a statistical relationship with OA at the lumbar or knee; J demonstrated a negative correlation with pelvic OA. Variation in OA can be explained by age, stature, body mass, and structural adaptation related to habitual use. The negative correlation between femoral torsional strength with OA suggests that long-term, repetitive physical work capacity in childhood may be protective against OA development later in life. The multifactorial aetiology of OA requires incorporating multiple lines of evidence to interpret individual or population health from bone samples.

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.

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.

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

Background

Recent 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.

Results

The 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.

Conclusions

The 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.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0336-y) contains supplementary material, which is available to authorized users.

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 18(th) 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.

Auricular surface aging: Worse than expected? A test of the revised method on a documented historic skeletal assemblage

This study presents results and recommendations arising from a blind test of the revised age estimation method for the auricular surface as proposed by Buckberry and Chamberlain ([2002] Am. J. Phys. Anthropol. 119:321-329). Auricular surfaces of 167 individuals from St. Bride's, London, a documented skeletal assemblage spanning the late 17th to early 19th century, were analyzed for the following traits: transverse organization, surface texture appearance, macroporosity, microporosity, and morphological changes to the apex. Composite scores of trait expressions were found to generally correlate with age and to show a positive association with known chronological age (P < 0.01). However, when composite scores were combined to define auricular surface phases, which ultimately assign age estimations, only three distinct developmental stages, compared with seven suggested by Buckberry and Chamberlain ([2002] Am. J. Phys. Anthropol. 119:321-329), could be identified and statistically supported, all showing a considerable degree of individual variation in age. The most well-defined stage in the St. Bride's assemblage was the new stage III, where the majority of individuals were older than 60 years, whereas middle-aged adults displayed a large variation in composite scores. These results provide little hope for a promising application of age-at-death estimation of auricular surface morphology traits with higher resolution, but rather suggest indications of broad stages of life.

The distal humerus--a blind test of Rogers' sexing technique using a documented skeletal collection

Continuous monitoring of existing methods of skeletal diagnosis allows improving the reliability of personal identification in forensic and archaeological contexts. This study reports on a blind test re-evaluating the sexing technique proposed by Rogers (8) involving the distal humerus. A total of 351 humeri (184 male, 167 female specimens) from the documented skeletal assemblage of St. Bride's, London, was analyzed for the following traits: trochlear constriction, trochlear symmetry, olecranon fossa shape, and angle of the medial epicondyle. Individual traits showed substantial sex-discriminatory capacity, with "olecranon fossa shape" being most consistently accurate (84.6%) in predicting sex. The combination of all four traits provided an overall accuracy of 79.1%, including those individuals assessed as "probable" male and female. This renders the technique useful for forensic applications. The distal humerus can be recommended for sex assessment in addition to more established markers, especially since this part of the skeleton is frequently well preserved.