Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750).

The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.

Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes.

BACKGROUND: Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period. RESULTS: Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria. CONCLUSIONS: Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.

The prevalence of cancer in Britain before industrialization.

BACKGROUND: To plan for cancer services in the future, the long view of cancer prevalence is essential. It might be suspected that cancer prevalence before tobacco and industrial revolution pollutants was quite different to today. METHODS: To quantify the degree to which cancer prevalence may be changing over time, the authors analyzed 143 skeletons from 6 cemeteries from the Cambridge area (6th-16th centuries). Visual inspection coupled with screening using both plain radiographs and computed tomography scans was used to detect malignant lesions. RESULTS: A total of 3.5% of individuals showed evidence for metastases. Factoring in modern data for the proportion of those with cancer that die with bone metastases, this suggests a minimum prevalence of all cancers at the time of death in medieval Britain to be approximately 9% to 14% of adults. CONCLUSIONS: This figure compares with a 40% to 50% prevalence of cancer at the time of death for modern Britain. The difference may be explained by the effects of modern carcinogens, the spread of viruses that trigger malignancy, industrial pollutants, and longer life expectancy. LAY SUMMARY: Until now, no one has been able to work out how common cancer was before the time people were exposed to tumor-inducing chemicals from tobacco and industrial factories. In this novel study, the authors have determined the percentage of people living in medieval Britain who had cancer metastases to bone at the time of their death and then compared that with modern data. It was found that cancer was approximately 25% as common in medieval times as it is today. This article suggests cancer was much more widespread in medieval times than was previously realized.

Medieval injuries: Skeletal trauma as an indicator of past living conditions and hazard risk in Cambridge, England.

OBJECTIVE: To explore how medieval living conditions, occupation, and an individual's role within society impacted their risk of skeletal trauma. MATERIALS: The skeletal remains of 314 individuals from medieval Cambridge that were buried in the parish cemetery of All Saints by the Castle (n = 84), the Augustinian friary (n = 75), and the cemetery of the Hospital of St John the Evangelist (n = 155) were analyzed. METHODS: Macroscopic examination and plain radiographs were used to classify fracture type. The causative mechanisms and forces applied to a bone were inferred based on fracture morphology. RESULTS: The skeletal trauma observed represents accidental injuries, likely sustained through occupational or everyday activities, and violence. The highest prevalence rate was observed on the individuals buried at All Saints by the Castle (44%, n = 37/84), and the lowest was seen at the Hospital of St John (27%, n = 42/155). Fractures were more prevalent in males (40%, n = 57/143) than females (26%, n = 25/95). CONCLUSIONS: Skeletal trauma was highest in All Saints parish burial ground, indicating that the poor, whether working urban or rurally, had the highest risk of injury. The pattern and types of fractures observed suggests that males experienced more severe traumatic events than females. However, females that were routinely involved in manual labor were also at increased risk of injury. SIGNIFICANCE: This article enhances our understanding of how traumatic injuries differed by age, sex, and burial locations in the medieval period. FURTHER RESEARCH: Additional comparative studies in different geographical regions are needed to determine how representative these findings are.

Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

Intrapopulation variation in lower limb trabecular architecture.

OBJECTIVES: Trabecular structure is frequently used to differentiate between highly divergent mechanical environments. Less is known regarding the response of the structural properties to more subtle behavioral differences, as the range of intrapopulation variation in trabecular architecture is rarely studied. Examining the extent to which lower limb trabecular architecture varies when inferred mobility levels and environment are consistent between groups within a relatively homogenous population may aid in the contextualization of interpopulation differences, improve detectability of sexual dimorphism in trabecular structure, and improve our understanding of trabecular bone functional adaptation. MATERIALS AND METHODS: The study sample was composed of adult individuals from three high/late medieval cemeteries from Cambridge (10th-16th c.), a hospital (n = 57), a parish cemetery (n = 44) and a friary (n = 14). Trabecular architecture was quantified in the epiphyses of the femur and tibia, using high resolution computed tomography. RESULTS: The parish individuals had the lowest bone volume fraction and trabecular thickness in most regions. Multiple sex differences were observed, but the patterns were not consistent across volumes of interest. DISCUSSION: Differences between the three groups highlight the great variability of trabecular bone architecture, even within a single sedentary population. This indicates that trabecular bone may be used in interpreting subtle behavioral differences, and suggests that multiple archaeological sites need to be studied to characterize structural variation on a population level. Variation in sex and group differences across anatomical locations further demonstrates the site-specificity in trabecular bone functional adaptation, which might explain why little consistent sexual dimorphism has been reported previously.

Evaluating macroscopic sex estimation methods using genetically sexed archaeological material: The medieval skeletal collection from St John's Divinity School, Cambridge.

OBJECTIVES: In tests on known individuals macroscopic sex estimation has between 70% and 98% accuracy. However, materials used to create and test these methods are overwhelming modern. As sexual dimorphism is dependent on multiple factors, it is unclear whether macroscopic methods have similar success on earlier materials, which differ in lifestyle and nutrition. This research aims to assess the accuracy of commonly used traits by comparing macroscopic sex estimates to genetic sex in medieval English material. MATERIALS AND METHODS: Sixty-six individuals from the 13th to 16th century Hospital of St John the Evangelist, Cambridge, were assessed. Genetic sex was determined using a shotgun approach. Eighteen skeletal traits were examined, and macroscopic sex estimates were derived from the os coxae, skull, and os coxae and skull combined. Each trait was tested for accuracy to explore sex estimates errors. RESULTS: The combined estimate (97.7%) outperformed the os coxae only estimate (95.7%), which outperformed the skull only estimate (90.4%). Accuracy rates for individual traits varied: Phenice traits were most accurate, whereas supraorbital margins, frontal bossing, and gonial flaring were least accurate. The preauricular sulcus and arc compose showed a bias in accuracy between sexes. DISCUSSION: Macroscopic sex estimates are accurate when applied to medieval material from Cambridge. However, low trait accuracy rates may relate to differences in dimorphism between the method derivative sample and the St John's collection. Given the sex bias, the preauricular sulcus, frontal bossing, and arc compose should be reconsidered as appropriate traits for sex estimation for this group.

East Anglian early Neolithic monument burial linked to contemporary Megaliths.

In the fourth millennium BCE a cultural phenomenon of monumental burial structures spread along the Atlantic façade. Megalithic burials have been targeted for aDNA analyses, but a gap remains in East Anglia, where Neolithic structures were generally earthen or timber. An early Neolithic (3762-3648 cal. BCE) burial monument at the site of Trumpington Meadows, Cambridgeshire, UK, contained the partially articulated remains of at least three individuals. To determine whether this monument fits a pattern present in megalithic burials regarding sex bias, kinship, diet and relationship to modern populations, teeth and ribs were analysed for DNA and carbon and nitrogen isotopic values, respectively. Whole ancient genomes were sequenced from two individuals to a mean genomic coverage of 1.6 and 1.2X and genotypes imputed. Results show that they were brothers from a small population genetically and isotopically similar to previously published British Neolithic individuals, with a level of genome-wide homozygosity consistent with a small island population sourced from continental Europe, but bearing no signs of recent inbreeding. The first Neolithic whole genomes from a monumental burial in East Anglia confirm that this region was connected with the larger pattern of Neolithic megaliths in the British Isles and the Atlantic façade.

Investigating the association between intestinal parasite infection and cribra orbitalia in the medieval population of Cambridge, UK.

OBJECTIVE: Cribra orbitalia is believed to be a skeletal indicator of chronic anaemia, scurvy, rickets or related metabolic diseases. It has been suggested that it may be used as a proxy indicator for intestinal parasite infection, as parasites often cause anaemia today. Our aim is to investigate this association in the medieval population of Cambridge, UK. MATERIALS: Individuals excavated from the cemeteries of the Augustinian friary and All Saints by the Castle parish church, and aged from 7 to adulthood. METHODS: We undertook parasite analysis of the pelvic sediment and control samples of 46 burials with intact orbital roofs. RESULTS: Human roundworm (Ascaris lumbricoides) and/or whipworm (Trichuris trichiura) were identified in the pelvic sediment of 22 individuals, and cribra orbitalia noted in 11 individuals. Barnards test showed no association between parasite infection and cribra orbitalia (p = .882). CONCLUSION: We found no association between infection and cribra orbitalia infection in this medieval adult population, calling into question this hypothesis, at least for adults. SIGNIFICANCE: High or low cribra orbitalia prevalence in adults should not be used to infer rates of intestinal parasite infection. LIMITATIONS: The individuals in the study were over the age of 7, with no younger children. It is possible that only parasites which cause marked anaemia (such as hookworm, schistosomiasis or malaria) may cause cribra orbitalia, while less marked anaemia from roundworm and whipworm may not do so. SUGGESTIONS FOR FURTHER RESEARCH: Repeating this study in younger children, when most cribra orbitalia appears to form.

Ancient Mycobacterium leprae genome reveals medieval English red squirrels as animal leprosy host.

Leprosy, one of the oldest recorded diseases in human history, remains prevalent in Asia, Africa, and South America, with over 200,000 cases every year.1,2 Although ancient DNA (aDNA) approaches on the major causative agent, Mycobacterium leprae, have elucidated the disease's evolutionary history,3,4,5 the role of animal hosts and interspecies transmission in the past remains unexplored. Research has uncovered relationships between medieval strains isolated from archaeological human remains and modern animal hosts such as the red squirrel in England.6,7 However, the time frame, distribution, and direction of transmissions remains unknown. Here, we studied 25 human and 12 squirrel samples from two archaeological sites in Winchester, a medieval English city well known for its leprosarium and connections to the fur trade. We reconstructed four medieval M. leprae genomes, including one from a red squirrel, at a 2.2-fold average coverage. Our analysis revealed a phylogenetic placement of all strains on branch 3 as well as a close relationship between the squirrel strain and one newly reconstructed medieval human strain. In particular, the medieval squirrel strain is more closely related to some medieval human strains from Winchester than to modern red squirrel strains from England, indicating a yet-undetected circulation of M. leprae in non-human hosts in the Middle Ages. Our study represents the first One Health approach for M. leprae in archaeology, which is centered around a medieval animal host strain, and highlights the future capability of such approaches to understand the disease's zoonotic past and current potential.

Genetic history of Cambridgeshire before and after the Black Death.

The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death.

Human Archaeological Dentin as Source of Polar and Less Polar Metabolites for Untargeted Metabolomic Research: The Case of Yersinia pestis.

Metabolomic approaches, such as in clinical applications of living individuals, have shown potential use for solving questions regarding the past when applied to archaeological material. Here, we study for the first time the potential of this Omic approach as applied to metabolites extracted from archaeological human dentin. Dentin obtained from micro sampling the dental pulp of teeth of victims and non-victims of Yersinia pestis (plague) from a 6th century Cambridgeshire site are used to evaluate the potential use of such unique material for untargeted metabolomic studies on disease state through liquid chromatography hyphenated to high-resolution mass spectrometry (LC-HRMS). Results show that small molecules of both likely endogenous and exogenous sources are preserved for a range of polar and less polar/apolar metabolites in archaeological dentin; however, untargeted metabolomic profiles show no clear differentiation between healthy and infected individuals in the small sample analysed (n = 20). This study discusses the potential of dentin as a source of small molecules for metabolomic assays and highlights: (1) the need for follow up research to optimise sampling protocols, (2) the requirements of studies with larger sample numbers and (3) the necessity of more databases to amplify the positive results achievable with this Omic technique in the archaeological sciences.

Tuberculosis before and after the Black Death (1346-1353 CE) in the Hospital of St John the Evangelist in Cambridge, England.

This research explores how the prevalence of tuberculosis (TB) in a medieval hospital was affected by the demographic and social changes that following the Black Death (1346-1353 CE), the initial years of the Second Plague Pandemic. To do this, skeletal remains of individuals buried at the Hospital of St John the Evangelist in Cambridge, England, that could be dated to living before (n = 77) or after (n = 55) the Black Death were assessed for evidence of TB (indicated by destructive lesions of the spine, ribs, large joints, and other recognised criteria). Overall, the odds of females having skeletal lesions caused by TB were over four times higher than males. No significant difference was detected in the prevalence rates in those who lived before and after the Black Death (7.8%, 6/77 before and 11.0%, 6/55 after). However, the odds of females having skeletal evidence of TB were over five times greater after the Black Death than they were before. These findings indicate that women may have been 1) more susceptible to TB, 2) surviving longer post-infection than men, and/or 3) that women with TB were more likely to be admitted to the Hospital especially following the Black Death. It is also possible that impairment due to TB infection may have been a contributing factor for entry into the Hospital for women but not men.

Metabolomics in archaeological science: A review of their advances and present requirements.

Metabolomics, the study of metabolites (small molecules of <1500 daltons), has been posited as a potential tool to explore the past in a comparable manner to other omics, e.g., genomics or proteomics. Archaeologists have used metabolomic approaches for a decade or so, mainly applied to organic residues adhering to archaeological materials. Because of advances in sensitivity, resolution, and the increased availability of different analytical platforms, combined with the low mass/volume required for analysis, metabolomics is now becoming a more feasible choice in the archaeological sector. Additional approaches, as presented by our group, show the versatility of metabolomics as a source of knowledge about the human past when using human osteoarchaeological remains. There is tremendous potential for metabolomics within archaeology, but further efforts are required to position it as a routine technique.

Examination of human osteoarchaeological remains as a feasible source of polar and apolar metabolites to study past conditions.

Metabolomics is a modern tool that aids in our understanding of the molecular changes in organisms. Archaeological science is a branch of archaeology that explores different archaeological materials using modern analytical tools. Human osteoarchaeological material are a frequent finding in archaeological contexts and have the potential to offer information about previous human populations, which can be illuminating about our current condition. Using a set of samples comprising different skeletal elements and bone structures, here we explore for the first time the possibility of extracting metabolites from osteoarchaeological material. Here, a protocol for extraction and measurement of extracted polar and less-polar/apolar metabolites by ultra-high performance liquid chromatography hyphenated to high resolution mass spectrometry is presented to measure the molecules separated after a reversed phase and hydrophilic interaction liquid chromatography column. Molecular information was obtained, showing that osteoarchaeological material is a viable source of molecular information for metabolomic studies.

Caring for the injured: Exploring the immediate and long-term consequences of injury in medieval Cambridge, England.

OBJECTIVE: To combine paleopathological and biomechanical analysis to reconstruct the impact that a severe skeletal injury had on an individual's ability to function and participate in medieval society. MATERIALS: Three medieval individuals from Cambridge, England with ante-mortem fractures to the lower limb were analyzed. METHODS: Plain X-rays were used to determine the degree of malunion, rotation and overlap of each fracture. Cortical bone architecture of the injured individuals and 28 uninjured controls were analyzed using micro-computed tomography (µCT). Clinical and functional consequences were examined using the Bioarcheology of Care framework. RESULTS: The mechanism of injury, the secondary complications, and the extent of the care received was reconstructed for each individual. Bilateral asymmetry in the cortical bone architecture revealed the long-term alterations to each individual's gait. CONCLUSION: Each of these individuals survived a severe injury resulting in chronic physical impairment, though not all would have been considered 'disabled'. SIGNIFICANCE: This research contributes to the discussion about medieval care provision and social constructions of disability by illustrating how an interdisciplinary approach provides insight into the experiences of those with physical impairments. The integration of µCT imaging within the Bioarcheology of Care model is a novel approach with great potential for application across the field. LIMITATIONS: Biomechanical analysis was restricted to cortical geometry. SUGGESTIONS FOR FUTURE RESEARCH: Further study of bilateral asymmetry in trabecular architecture could complement our understanding of altered loading modalities in past societies.

Intestinal parasite infection in the Augustinian friars and general population of medieval Cambridge, UK.

OBJECTIVE: To investigate how lifestyle may have impacted the risk of contracting intestinal parasites in medieval England . Regular clergy (such as those living in monasteries) and the lay population form interesting groups for comparison as diet and lifestyle varied significantly. Monasteries were built with latrine blocks and hand washing facilities, unlike houses of the poor. MATERIALS: Sediment samples from the pelvis, along with control samples from feet and skull, of 19 burials of Augustinian Friars (13th-16th century), and 25 burials from All Saints by the Castle parish cemetery (10th-14th century), Cambridge. METHODS: We analysed the sediment using micro-sieving and digital light microscopy to identify the eggs of intestinal parasites. RESULTS: Parasite prevalence (roundworm and whipworm) in the Augustinian friars was 58%, and in the All Saints by the Castle parishioners just 32% (Barnards Test score statistic 1.7176, p-value 0.092). CONCLUSIONS: It is interesting that the friars had nearly double the infection rate of parasites spread by poor hygiene, compared with the general population. We consider options that might explain this difference, and discuss descriptions and treatment of intestinal worms in medical texts circulating in Cambridge during the medieval period. SIGNIFICANCE: This is the first study to compare prevalence of parasite infection between groups with different socioeconomic status from the same location. LIMITATIONS: Quality of egg preservation was suboptimal, so our data may under-represent the true prevalence. SUGGESTIONS FOR FURTHER RESEARCH: Larger studies with greater statistical power, covering different time periods and regions.

Assessing the relative benefits of imaging with plain radiographs and microCT scanning to diagnose cancer in past populations.

OBJECTIVE: To determine the degree to which plain radiographs (x-rays) and microCT scans can improve accuracy in the diagnosis of cancer in human remains from past populations. MATERIALS: The skeletal remains of 143 individuals from medieval Cambridgeshire, dating from 6th-16th century CE. METHODS: Visual inspection of the skeletons for lesions compatible with malignancy, coupled with plain radiographs and microCT scans of the pelvis, femora and vertebra. RESULTS: Three individuals had visually apparent metastases on their skeletons. Plain radiographs did not identify further individuals with cancer, but did show further lesions in bones with normal external appearance. MicroCT scans identified cancer in two further individuals with normal visual appearance and normal plain radiographs. CONCLUSIONS: Imaging human skeletal remains increases the detection rate of cancer in human skeletal remains. We found microCT scanning to be a much more sensitive imaging modality than plain radiography. It improved our diagnostic accuracy and enabled us to more reliably distinguish between malignant lesions and taphonomic change. SIGNIFICANCE: Future studies investigating the prevalence and nature of malignancy in past populations would benefit from systematic microCT scanning of pelvis, femora and vertebrae of skeletons to optimise their diagnostic accuracy. LIMITATIONS: MicroCT scanning is more expensive than plain radiographs, and may not be easily accessible to biological anthropologists. SUGGESTIONS FOR FURTHER RESEARCH: To apply this approach to skeletal series from different time periods and geographical regions, where the types of cancer existing in the local population may differ from those we studied in medieval Britain.