Finding Mycenaeans in Minoan Crete? Isotope and DNA analysis of human mobility in Bronze Age Crete.

We undertook a large-scale study of Neolithic and Bronze Age human mobility on Crete using biomolecular methods (isotope analysis, DNA), with a particular focus on sites dating to the Late Bronze Age ('Late Minoan') period. We measured the strontium and sulphur isotope values of animal remains from archaeological sites around the island of Crete to determine the local baseline values. We then measured the strontium and sulphur values of humans from Late Neolithic and Bronze Age sites. Our results indicate that most of the humans have sulphur and strontium isotope values consistent with being local to Crete, showing no evidence for a wide-scale movement of people from the Greek mainland or other areas away from Crete in these time periods. However, we found four individuals from the late Bronze Age (Late Minoan III) cemetery of Armenoi with sulphur isotope values not typically found in Crete and are instead consistent with an origin elsewhere. This cemetery at Armenoi also has one of only a few examples of the newly adopted Mycenaean Linear B script on Crete found outside of the palace sites, pointing to an influence (trade and possible migration) from the mainland, which may then be the place of origin of these four individuals. DNA (mtDNA) studies of eight Late Bronze Age individuals from Armenoi have results consistent with people living in Aegean region at this time and cannot be used to distinguish between individuals from Crete ('Minoans') and the Greek mainland ['Mycenaeans']).

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.

Potential adaptations for bipedalism in the thoracic and lumbar vertebrae of Homo sapiens: A 3D comparative analysis.

A number of putative adaptations for bipedalism have been identified in the hominin spine. However, it is possible that some have been overlooked because only a few studies have used 3D and these studies have focused on cervical vertebrae. With this in mind, we used geometric morphometric techniques to compare the 3D shapes of three thoracic and two lumbar vertebrae of Homo sapiens, Pan troglodytes, Gorilla gorilla, and Pongo pygmaeus. The study had two goals. One was to confirm the existence of traits previously reported to distinguish the thoracic and lumbar vertebrae of H. sapiens from those of the great apes. The other was to, if possible, identify hitherto undescribed traits that differentiate H. sapiens thoracic and lumbar vertebrae from those of the great apes. Both goals were accomplished. Our analyses not only substantiated a number of traits that have previously been discussed in the literature but also identified four traits that have not been described before: (1) dorsoventrally shorter pedicles in the upper thoracic vertebrae; (2) dorsoventrally longer laminae in all five of the vertebrae examined; (3) longer transverse processes in the upper thoracic vertebrae; and (4) craniocaudally 'pinched' spinous process tips in all of the vertebrae examined. A review of the biomechanical literature suggests that most of the traits highlighted in our analyses can be plausibly linked to bipedalism, including three of the four new ones. As such, the present study not only sheds further light on the differences between the spines of H. sapiens and great apes but also enhances our understanding of how the shift to bipedalism affected the hominin vertebral column.

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.

Effects of osteoarthritis on age-at-death estimates from the human pelvis.

OBJECTIVES: This study examined the degree of error in age-at-death estimates when osteoarthritis (OA) is present in three separate pelvic joint areas: (1) the pubic symphysis, (2) the auricular surface, and (3) the acetabulum from a modern known-age European cemetery sample of adults. MATERIALS AND METHODS: Age-at-death ranged from 17 to 79 years (x̄ =50.9 years; n = 252). OA in the pelvic joints was evaluated using standard ranked categorical scoring. Composite OA scores were derived through principal component analysis. Blind age assessments and all analyses were performed separately by region. Error between adult age groups (young, middle, old) and between OA severity groups (low, middle, high) was evaluated using one-way ANOVAs with post-hoc testing, ordinary least squares regression, and transition analysis with a cumulative probit model. Ages-at-transition were compared with Nphases2. RESULTS: Three significant results emerge. First, OA severity has an effect on the accuracy of age estimates from os coxa joints in this sample. Second, this influence is most significant for different age cohorts in each joint region, demonstrating that varied rates of arthritic trait progression occur between the auricular surface, pubic symphyses, and acetabulum. Third, those with OA appear to be aging faster, a consistent trend among the os coxa regions. CONCLUSIONS: These results have significant consequences for understanding the rate of bone remodeling in relation to disease, aging, and the evaluation of skeletal age indicators.

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.

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.

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.

Out of the North Sea: the Zeeland ridges Neandertal.

In 2001, a portion of human frontal bone was discovered in sediments extracted from the bottom of the North Sea, 15km off the coast of the Netherlands. The extraction zone is located in the so-called Zeeland Ridges area located at 51 degrees 40' northern latitude and 3 degrees 20' eastern longitude. The specimen was dredged up from sediments containing Late Pleistocene faunal remains and Middle Palaeolithic artefacts, including well-finished small handaxes and Levallois flakes. The details of the supraorbital morphology, as well as the quantitative assessment of the shape of the external surface of the squama using traditional and 3D geometric morphometrics, unambiguously assign the Zeeland Ridges frontal bone to Homo neanderthalensis. Carbon and nitrogen isotopic analysis indicate that the Zeeland Ridges hominin, like other Neandertals, was highly carnivorous and does not show evidence for the consumption of aquatic foods. A lesion on the outer table and diploic layer of the bone in the area of the supratoral sulcus can be interpreted as the result of an intradiploic epidermoid cyst, a type of neoplasm diagnosed for the first time in Neandertal remains. So far, the Zeeland Ridges Neandertal is the first Pleistocene fossil hominin found under seawater and the first recorded in the Netherlands.

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 George's 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).

Investigating the specificity of periosteal reactions in pathology museum specimens.

The relationship between periosteal new bone formation and a number of infectious and metabolic conditions frequently seen in archeological human skeletal remains was investigated by studying human long bones demonstrating periosteal new bone formation archived in two London, UK, pathology museums: the St. George's Hospital Pathology Museum and the Hunterian Museum. The samples were subjected to macroscopic and radiographic analysis to determine if the characteristics of their periosteal lesions were specific to the corresponding disease states. The results demonstrated that no qualitative or quantitative characteristics of the periosteal reactions emerged that were specific to individual disease states. It was established that disease progression, rather than disease type, was the most important determinant of periosteal lesion appearance. A critical analysis of the bioarcheology literature pertaining to the recording and interpretation of periosteal reactions determined that the varied pathogenesis of periosteal new bone formation has been largely ignored in favor of a diagnosis of "nonspecific infection." Assumptions regarding the infectious etiology of periosteal lesions have become embedded into the bioarcheology literature potentially skewing the results of skeletal population-based paleoepidemiological studies.

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.