An assemblage deposited at Clare College, Cambridge, England, in 1879-1885 represents the largest archaeologically recovered assemblage from a nineteenth-century Cambridge college. It contains a wide range of material deriving from the corporate collegiate household, including ceramics, glassware, clay tobacco pipes and other materials. This material comprises a mixture of corporate and individual material, which can be interpreted in light of the predominantly young adult male college population, while also shedding light on marginalized groups, particularly women and servants. It also indicates distinctions between collegiate and domestic material culture in Cambridge.

The origin and spread of consecutive outbreaks of the second plague pandemic in Europe (14th to 18th c.) are still poorly understood, although over one hundred ancient Yersinia pestis genomes and a vast corpus of documentary data have been collected. For most ancient genomes, radiocarbon (RC) dates regularly spanning more than 100 y are the only temporal information. This hampers an association with historically recorded outbreaks and limits our understanding of the microevolution and phylogeography of Y. pestis in the four centuries following the European Black Death (1347–1353). Here, we present new genomic evidence of the Second Pandemic from 11 sites in Europe, yielding 11 full and 15 lower-coverage genomes of Y. pestis dating to 1349–1710. To improve the dating information of our newly sequenced and previously published Y. pestis genomes, we present “Phylogenetically Informed Radiocarbon Modeling”, an approach that integrates chronological information retrieved from phylogenetic analysis with respective RC dates, leading to more accurate and precise dating intervals. Together with a fine-grained analysis of recorded plague outbreaks, this allows us to tentatively associate 75 genomes of the Second Pandemic with historically documented plague outbreaks.

Archaeological investigations at Clare College, Cambridge, between 2014 and 2021 allow a much greater understanding of the fourteenth to seventeenth-century college than has previously been possible. The extent and layout of the later Medieval quadrangle can be reconstructed with some accuracy. The western range was probably not constructed until the mid-fifteenth century and was c. 9.7 m wide (8.5 m internally). The ground floor was c. 0.4 m lower than the ground surface in the central court, and c. 0.2 m higher than the ground to the west. The western range incorporated considerable quantities of brick and the floor of the Master's Lodge was supported by posts on stone pads. The ground was remodelled in the early/mid-seventeenth century, around the time the modern college buildings began to be constructed, with brick floors and plastered walls, and went out of use in the late seventeenth century. While the development of Clare College is usually thought of as two phases, of later Medieval buildings that were replaced by Early Modern structures, there was effectively an intermediate period that was a mixture of the two that existed in several stages over a 130 year period, between 1638 and 1769.

Human betaherpesviruses 6A and 6B (HHV-6A/6B) are DNA viruses, which integrate into the human genome, and are best known to cause "sixth disease." Despite their recent discovery (1980s), they were speculated to have a much longer history within the human population than modern data suggest. We present the first 11 ancient genomes of HHV-6A and HHV-6B, dating as far back as the 8th to 6th century BCE. We demonstrate that large fractions of current HHV-6 diversity were already established by the 14th century CE. Our data corroborate that HHV-6A/6B integrations stem from ancient founder events. In addition, we show that all known inherited chromosomally integrated HHV-6A clades were already represented in historical populations, confirming that HHV-6A no longer integrates into the germ line within populations of European ancestry and likely endogenized in early human history.

The analysis of stable carbon and nitrogen isotopes in bone collagen can reveal aspects of diet and how this may change between periods and places. Here, the authors apply a 'whole-town' approach to isotopic analysis, to characterise and explore variation in diet within medieval Cambridge and its hinterland. By adopting this approach, and a robust isotopic baseline, the authors argue that the number of confounding variables that typically plague archaeometric research are reduced, allowing for more nuanced interpretation of data. For medieval Cambridge, this nuance comes in the form of inter-site comparisons in the lived experience of social differentiation.

The Black Death epidemic of Yersinia pestis (1347-50 CE) killed about half the population of England, and many historical changes have been ascribed to it. But we still know surprisingly little about how the epidemic actually affected people's daily lives. This study reports results from a broad bioarchaeological study, with 18 skeletal and molecular indicators from 336 adults from Cambridge, England (940-1561 CE). Results reveal two major findings. First, although the epidemic killed millions, no dramatic changes in skeletal indicators of health and lifestyle are directly ascribable to the epidemic. Most indicators either remained stable, or changed in response to other known historical trends. Traumatic though the plague was, it did not transform medieval people's health and lifeways radically. Secondly, there were important long-term health trends beginning before the Black Death, notably a decline in stature. This may be due to a general 14th -century environmental and economic deterioration which left the population more vulnerable to novel epidemic diseases.

In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, however, sediments are not always collected during excavation. In this study, we analyzed an overlooked but abundant resource in archaeological collections - sediments adhered to bone. We performed metagenomics and metaproteomics analysis on sediment from several human skeletal elements, originating from Neolithic to Medieval sites in England. We were able to reconstruct a partial human genome, the genetic profile of which matches that recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular, we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material that is usually ignored or discarded, can be used to reveal information about the individual and the environmental conditions at the time of their death.

The Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today Great Britain. While there is written evidence of high mobility into and out of Britain for administrators, traders, and the military, the impact of imperialism on local, rural population structure, kinship, and mobility is invisible in the textual record. The extent of genetic change that occurred in Britain during the Roman military occupation remains underexplored. Here, using genome-wide data from 52 ancient individuals from eight sites in Cambridgeshire covering the period of Roman occupation, we show low levels of genetic ancestry differentiation between Romano-British sites and indications of larger populations than in the Bronze Age and Neolithic. We find no evidence of long-distance migration from elsewhere in the Empire, though we do find one case of possible temporary mobility within a family unit during the Late Romano-British period. We also show that the present-day patterns of genetic ancestry composition in Britain emerged after the Roman period.

Human betaherpesviruses 6A and 6B are double-stranded DNA viruses, specialised in infecting humans and are best known as the main causative pathogens of the common childhood infection “sixth disease”. Despite only being discovered in the 1980s, these viruses are speculated to have a much longer and more complex history within the human population than available modern data make clear. The viruses are carried by large fractions of the human population and can integrate into the human genome, leading to a wide range of clinical manifestations of varied severity. Here, we present the first nine full and two partial ancient genomes of HHV-6A and 6B, dating as far back as the Italian Iron Age (ca. 1100–600 BCE). We demonstrate that large fractions of the current HHV-6 diversity were already well established in the human population by the 14th century CE. Our data suggests that HHV-6B integrated into the human genome at the latest before the 1st-6th century CE, with two integrated clades being populated by ancient DNA genomes in our phylogeny, which further supports that they originated from likely much older ancient founder events. Additionally, we show that all known inherited chromosomally integrated (ici-)HHV-6A clades were already represented in European historical populations, confirming that ici-HHV-6A no longer integrates into the human germline within populations of European ancestry and likely endogenized in early human history. Finally, our results demonstrate the unique suitability of archaeological remains and ancient DNA for the study of the evolution of integrated viruses in human populations. ### Competing Interest Statement The authors have declared no competing interest.

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.

Health inequality is not only a major problem today; it left its mark upon past societies too. For much of the past, health inequality has been poorly studied, mostly because bioarchaeologists have concentrated upon single sites rather than a broader social landscape. This article compares 476 adults in multiple locations of medieval Cambridge (UK). Samples include ordinary townspeople (All Saints), people living in a charitable institution (the Hospital of St. John), and members of a religious order (the Augustinian Friary). These groups shared many conditions of life, such as a similar range of diseases, risk of injury, and vertebral disk degeneration. However, people living on charity had more indicators of poor childhood health and diet, lower adult stature, and a younger age at death, reflecting the health effects of poverty. In contrast, the Augustinian friars were members of a prosperous, well-endowed religious house. Compared with other groups, they were taller (perhaps a result of a richer diet during their adolescent growth period); their adult carbon and nitrogen isotope values are higher, suggesting a diet higher in terrestrial and/or marine animal protein; and they had the highest prevalence of foot problems related to fashionable late medieval footwear. As this illustrates, health inequality will take particular forms depending upon the specificities of a social landscape; except in unusual circumstances where a site and its skeletal samples represent a real cross-section of society, inequality is best investigated by comparison across sites.

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.

Medieval hospitals were founded to provide charity, but poverty and infirmity were broad and socially determined categories and little is known about the residents of these institutions and the pathways that led them there. Combining skeletal, isotopic and genetic data, the authors weave a collective biography of individuals buried at the Hospital of St John the Evangelist, Cambridge. By starting with the physical remains, rather than historical expectations, they demonstrate the varied life courses of those who were ultimately buried in the hospital's cemetery, illustrating the diverse faces of medieval poverty and institutional notions of charity. The findings highlight the value of collective osteobiography when reconstructing the social landscapes of the past.

The extent of the devastation of the Black Death pandemic (1346-53) 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 local scale in the context of the social stratification of medieval communities. Here we study 275 newly reported ancient genomes from later medieval and post-medieval Cambridgeshire, from individuals buried before, during, and after the Black Death. The majority of individuals examined had local genetic ancestries. 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. Accounting for the genetic component for height accentuates the disparities between social groups in stature estimated from long bones, as a proxy for health and the quality of life. While we detect long-term shifts in local genetic ancestry in Cambridgeshire that either pre- or postdate the Black Death, we find no evidence of major changes in genetic ancestry nor, in contrast to recent claims, higher differentiation of immune loci between cohorts living before and after the Black Death.

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.

Although dozens of ancient Yersinia pestis genomes and a vast corpus of documentary data are available, the origin and spread of consecutive outbreaks of the Second Plague Pandemic in Europe (14th–18th c.) are still poorly understood. For the majority of ancient genomes, only radiocarbon dates spanning several decades are available, hampering an association with historically recorded plague outbreaks. Here, we present new genomic evidence of the Second Pandemic from 11 sites in England, Estonia, the Netherlands, Russia, and Switzerland yielding 11 Y. pestis genomes with >4-fold mean coverage dating to between 1349 and 1710. In addition, we present a novel approach for integrating the chronological information retrieved from phylogenetic analysis with their respective radiocarbon dates, based on a novel methodology offering more precise dating intervals. Together with a fine-grained analysis of documentarily recorded plague outbreaks, this allows us to tentatively associate all available Y. pestis genomes of the Second Pandemic with historically documented plague outbreaks. Through these combined multidisciplinary analytical efforts, our newly sequenced genomes can be attributed to the Black Death in Cambridge (England), the pestis tertia or pestis quarta in the late 14th century (Estonia), previously unknown branches emerging in the 15th century (Estonia, the Netherlands and England), and a widespread pandemic in Eastern Europe around 1500 (western Russia), which all seem to have originated from one or multiple reservoirs located in Central Europe. While the latter continued to harbour a major Y. pestis lineage at least until the 1630s, represented by new genomes of the Thirty Years’ War plague (Switzerland), another lineage consecutively spread into Europe between the 17th and 18th century from the Ottoman Empire, as evidenced by a genome associated with the Great Northern War plague (Estonia). By combining phylogenetic analysis with a systematic historical reconstruction based on textual sources and an innovative phylogenetically informed radiocarbon modelling (PhIRM), we offer a new groundbreaking interdisciplinary approach that solves several fundamental methodological challenges associated with phylogenetic and spatio-temporal reconstruction of historical pandemics.

The Augustinian friary in Cambridge, England, was founded in the 1280s and dissolved in 1538. Investigations in 1908–9 and 2016–19 have revealed much of the friary cloister, with evidence for an initial late thirteenth–mid-fourteenth-century phase, a major phase of construction in the mid–late fourteenth century and some fifteenth-century construction. This paper will primarily consider what can be reconstructed of the claustral buildings, complemented by what is known of the rest of the friary site. The friary will also be contextualised in terms of mendicant beliefs and anti-fraternal criticisms.

The Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today the United Kingdom. While there is written evidence of high mobility into and out of Britain for administrators, traders and the military, the impact of imperialism on local population structure is invisible in the textual record. The extent of genetic change that occurred in Britain before the Early Medieval Period and how closely linked by genetic kinship the local populations were, remains underexplored. Here, using genome-wide data from 52 ancient individuals from Cambridgeshire, we show low levels of genetic ancestry differentiation between Romano-British sites and lower levels of runs of homozygosity over 4 centimorgans (cM than in the Bronze Age and Neolithic. We find fourteen cases of genetic relatedness within and one between sites without evidence of patrilineal dominance and one case of temporary mobility within a family unit during the Late Romano-British period. We also show that the modern patterns of genetic ancestry composition in Modern Britain emerged after the Roman period.