A genomic and historical synthesis of plague in 18th century Eurasia.

Plague continued to afflict Europe for more than five centuries after the Black Death. Yet, by the 17th century, the dynamics of plague had changed, leading to its slow decline in Western Europe over the subsequent 200 y, a period for which only one genome was previously available. Using a multidisciplinary approach, combining genomic and historical data, we assembled Y. pestis genomes from nine individuals covering four Eurasian sites and placed them into an historical context within the established phylogeny. CHE1 (Chechnya, Russia, 18th century) is now the latest Second Plague Pandemic genome and the first non-European sample in the post-Black Death lineage. Its placement in the phylogeny and our synthesis point toward the existence of an extra-European reservoir feeding plague into Western Europe in multiple waves. By considering socioeconomic, ecological, and climatic factors we highlight the importance of a noneurocentric approach for the discussion on Second Plague Pandemic dynamics in Europe.

Economic access influences degenerative spine disease outcomes at rural Late Medieval Villamagna (Lazio, IT).

OBJECTIVES: Degenerative joint disease in the spine is heavily influenced by genetic, environmental, and epigenetic factors, as well as exacerbated by physical activity and injury. The objective of this study was to investigate the multivariate relationship between known predictors of degenerative joint disease in the spine, such as age and sex, with mortuary indicators of economic access such as grave inclusions, burial location, and burial type. MATERIALS AND METHODS: The presence and severity of vertebral osteophytosis (VO) and vertebral osteoarthritis (VOA) was recorded for the vertebral columns of N = 106 adult individuals from the Late Medieval period at the rural monastery of San Pietro at Villamagna in Lazio, Italy (1300-1450 AD). Multiple skeletal indicators of degenerative joint disease, morphological sex, and age were compared with differences in mortuary treatment across four regions of the spine. RESULTS: There are marked differences in severe joint disease outcome between groups with more and less economic access. Relative risk ratios suggest that males and females with less economic access have elevated risk for VO and VOA in specific spine regions, although this effect is reduced among females. DISCUSSION: Current research on the consequences of economic and social inequality point to the important role of economic inequality in shaping disease outcomes. Our results suggest that biocultural effects of reduced economic access at the intraclass level may increase vulnerability to the downstream effects of risk exposure (e.g., biomechanical injure, physical activity, biochemical imbalance), and ultimately increase the risk and prevalence for severe degenerative disease outcomes in medieval Italy.

Making sense of medieval mouths: Investigating sex differences of dental pathological lesions in a late medieval Italian community.

OBJECTIVES: Bioarchaeological investigations of sex-based differences in the prevalence of dental pathological lesions, particularly caries, have drawn considerable attention, and out of this work, two dominant models have emerged. Traditionally, the first model interprets sex-related patterns in caries as a product of gendered differences in diet. A more recent model interprets a generally higher propensity for caries prevalence in females in light of reproductive ecology. To test the hypothesis that females have higher risk of caries in accordance with reproductive ecology, we examined and analyzed caries prevalence and other potentially synergistic oral pathological lesions in a late medieval (A.D. 1300-1500) Italian archaeological sample. MATERIALS AND METHODS: We examined sex- and age-related prevalence in caries and other oral pathological lesions in a late medieval Italian skeletal assemblage excavated from Villamagna consisting of 38 females and 37 males (n = 1,534 teeth). We examined age- and sex-related patterns in six dental traits: antemortem tooth loss, caries, calculus, periapical inflammation, tooth wear, and periodontitis. RESULTS: Significant age-related increases in antemortem tooth loss, caries, calculus, and tooth wear were observed in both males and females. However, there was a lack of expected sex differences in oral pathological lesions, with instead older males exhibiting significantly more antemortem tooth loss and corrected caries than females. DISCUSSION: Results are discussed in relation to the ethnohistoric context of medieval rural dietary practices as well as biomedical salivary literature, which suggest that dietary changes throughout the life course may have facilitated trade-offs that buffered females from higher rates of dental pathological lesions.

Dental calculus indicates widespread plant use within the stable Neanderthal dietary niche.

The ecology of Neanderthals is a pressing question in the study of hominin evolution. Diet appears to have played a prominent role in their adaptation to Eurasia. Based on isotope and zooarchaeological studies, Neanderthal diet has been reconstructed as heavily meat-based and generally similar across different environments. This image persists, despite recent studies suggesting more plant use and more variation. However, we have only a fragmentary picture of their dietary ecology, and how it may have varied among habitats, because we lack broad and environmentally representative information about their use of plants and other foods. To address the problem, we examined the plant microremains in Neanderthal dental calculus from five archaeological sites representing a variety of environments from the northern Balkans, and the western, central and eastern Mediterranean. The recovered microremains revealed the consumption of a variety of non-animal foods, including starchy plants. Using a modeling approach, we explored the relationships among microremains and environment, while controlling for chronology. In the process, we compared the effectiveness of various diversity metrics and their shortcomings for studying microbotanical remains, which are often morphologically redundant for identification. We developed Minimum Botanical Units as a new way of estimating how many plant types or parts are present in a microbotanical sample. In contrast to some previous work, we found no evidence that plant use is confined to the southern-most areas of Neanderthal distribution. Although interpreting the ecogeographic variation is limited by the incomplete preservation of dietary microremains, it is clear that plant exploitation was a widespread and deeply rooted Neanderthal subsistence strategy, even if they were predominately game hunters. Given the limited dietary variation across Neanderthal range in time and space in both plant and animal food exploitation, we argue that vegetal consumption was a feature of a generally static dietary niche.

Leprosy in a Lombard-Avar cemetery in central Italy (Campochiaro, Molise, 6th-8th century AD): ancient DNA evidence and demography.

BACKGROUND: The study of past infectious diseases increases knowledge of the presence, impact and spread of pathogens within ancient populations. AIM: Polymerase chain reaction (PCR) was used to examine bones for the presence of Mycobacterium leprae ancient DNA (aDNA) as, even when leprosy is present, bony changes are not always pathognomonic of the disease. This study also examined the demographic profile of this population and compared it with two other populations to investigate any changes in mortality trends between different infectious diseases and between the pre-antibiotic and antibiotic eras. SUBJECTS AND METHODS: The individuals were from a site in Central Italy (6th-8th CE) and were examined for the presence of Mycobacterium leprae aDNA. In addition, an abridged life mortality table was constructed. RESULTS: Two individuals had typical leprosy palaeopathology, and one was positive for Mycobacterium leprae aDNA. However, the demographic profile shows a mortality curve similar to that of the standard, in contrast to a population that had been subjected to bubonic plague. CONCLUSIONS: This study shows that, in the historical population with leprosy, the risk factors for health seem to be constant and distributed across all age classes, similar to what is found today in the antibiotic era. There were no peaks of mortality equivalent to those found in fatal diseases such as the plague, probably due to the long clinical course of leprosy.

A revision of hominin fossil teeth from Fontana Ranuccio (Middle Pleistocene, Anagni, Frosinone, Italy).

The Fontana Ranuccio hominin teeth (FR, Latium, Italy) are dated to the Middle Pleistocene. In previous studies these teeth were classified as two lower (left and right) second molars, one lower left central incisor and a badly worn incisor crown, the exact position of which could not be determined. In 2012 these remains were acquired by the Anthropological Service of S.B.A.L. (Italian Ministry of Culture) and for this reason re-analysed. In a thorough revision we have reassessed them both morphologically and dimensionally as two lower (left and right) first molars, one lower left lateral incisor and a possible upper left canine. The comparison with penecontemporaneous and diachronic samples shows that the Fontana Ranuccio teeth are morphologically similar to Atapuerca-Sima de los Huesos, Arago XIII and Neanderthal samples.

Metastatic cancer and endentulism: Exploring comorbidity to assist with differential diagnosis in a case from Vico nel Lazio (Fr, Italy), 13th-15th century CE.

OBJECTIVE: To differentially diagnose cranial lesions noted on a medieval skeleton and explore the importance of comorbidity. MATERIALS: A skull of an adult female with osteolytic and osteoblastic lesions, edentulism, and an ectopic tooth from an ossuary of the Church of Santa Maria in Vico del Lazio, Frosinone Italy, dating to the Middle Ages. METHODS: Macroscopic observations of the remains, CT scan, and differential diagnosis was undertaken. RESULTS: A diagnosis of metastatic cancer (potentially breast cancer) or metastatic neuroblastoma (NBL) is offered. CONCLUSIONS: Considering the noted comorbidities, this case might represent a rare case of metastatic neuroblastoma. SIGNIFICANCE: The exploration of comorbidity, in this case the presence of metastatic carcinoma and edentulism, has tremendous potential to expand our knowledge about cancer in the past. LIMITATIONS: Lack of postcranial elements. SUGGESTIONS FOR FURTHER RESEARCH: Clinical and paleopathological investigation of comorbidity in modern and archeological populations to develop an evolutionary perspective on the presence of cancer in the past.

A new methodology to estimate flat foot in skeletal remains - the example of Mediterranean collections.

Flat feet (pes planus) are considered a postural defect caused by the collapse of the longitudinal arch, producing complete or near-complete contact of the sole of the foot with the ground. Pes planus has been well-studied in clinical literature and paleoanthropology but has not been approached extensively in bioarchaeology. The main difficulty is related to the diagnosis of this pathology based exclusively on bone remains. In this work, we propose a metric and morphological method to discriminate flat foot in dry bones. Thus, we studied 390 pairs of adult feet in a fair state of preservation from archaeological contexts from Spain, Italy, and Oman. Morphological variability, angles, and dimensions of both the normal bones and the bones displaying flat foot characteristics were analyzed. We found a correlation between the presence of flat foot and some morphological and metric features, mainly in the subtalar and Chopart joints. These results are expressed through a combination of morphological and metric variables, which are useful to discriminate between these two groups. No markedly significant differences of flat foot frequencies between the Spanish and Italian series were found across centuries. However, we noticed a notable increase of the prevalence of flat foot in the contemporary collection, possibly due to the consequences of a rise in life expectancy and modern styles of footwear.

Environmental implications and evidence of natural products from dental calculi of a Neolithic-Chalcolithic community (central Italy).

In this contribution, we investigated the role of plants in the prehistoric community of Casale del Dolce (Anagni, FR, central Italy), through microparticles recovered from dental calculus. The finding of a great amount of pollen types, even in form of compact lumps, could indicate use of natural substances, such as honeybee products and/or conifer resins. This plant-microremain record also suggested environmental implications relative to the Neolithic and Chalcolithic period. Additionally, the stability of the tartar microenvironment had preserved starches and other microparticles, such as one epidermal trichome, a sporangium, and fragments of plant tissue, rarely detected in ancient dental calculus. The detection of secondary metabolites in the ancient matrix confirmed the familiarity of this community with plant resources. All these data supply various interesting food for thought and expand the knowledge about the potential of dental calculus in archaeological and archaeobotanical fields with a special focus on palaeoecology.

Biological history of an Italian prehistoric community and the population of the central Italy during the 1st millennium BCE.

Understanding the population of Central Italy during the 1st millennium BCE is a crucial topic in the biological history of the Mediterranean basin. This period saw the emergence of the Etruscan and Roman cultures which had a significant impact on the bio-cultural history of the region. In this study, we analyse a prehistoric population from Caracupa (Iron Age, Latium, Central Italy). The results suggest an overall good level of health for the population. Despite this, some musculoskeletal changes related to biomechanical stressors were observed, probably as the result of strenuous physical activity. The results of a Simple Matching analysis of intragroup distance distributions suggest potential model of kinship structures and lineages. This may be due to the relative geographic isolation of the Caracupa population. Furthermore, in order to investigate the wider population of Central Italy during the 1st millennium BCE, we have constructed a population pattern using genetic and phenotypic skeletal and dental traits. The comparison between Central Italy and more isolated populations indicated a divergence between the Western and Eastern sides of Central Italy. However, we do not exclude a probable common genetic substratum for all Central Italian populations during the 1st millennium BCE.

Ancient Rome: A genetic crossroads of Europe and the Mediterranean.

Ancient Rome was the capital of an empire of ~70 million inhabitants, but little is known about the genetics of ancient Romans. Here we present 127 genomes from 29 archaeological sites in and around Rome, spanning the past 12,000 years. We observe two major prehistoric ancestry transitions: one with the introduction of farming and another prior to the Iron Age. By the founding of Rome, the genetic composition of the region approximated that of modern Mediterranean populations. During the Imperial period, Rome's population received net immigration from the Near East, followed by an increase in genetic contributions from Europe. These ancestry shifts mirrored the geopolitical affiliations of Rome and were accompanied by marked interindividual diversity, reflecting gene flow from across the Mediterranean, Europe, and North Africa.

Digital reconstruction of the Ceprano calvarium (Italy), and implications for its interpretation.

The Ceprano calvarium was discovered in fragments on March 1994 near the town of Ceprano in southern Latium (Italy), embedded in Middle Pleistocene layers. After reconstruction, its morphological features suggests that the specimen belongs to an archaic variant of H. heidelbergensis, representing a proxy for the last common ancestor of the diverging clades that respectively led to H. neanderthalensis and H. sapiens. Unfortunately, the calvarium was taphonomically damaged. The postero-lateral vault, in particular, appears deformed and this postmortem damage may have influenced previous interpretations. Specifically, there is a depression on the fragmented left parietal, while the right cranial wall is warped and angulated. This deformation affected the shape of the occipital squama, producing an inclination of the transverse occipital torus. In this paper, after X-ray microtomography (µCT) of both the calvarium and several additional fragments, we analyze consistency and pattern of the taphonomic deformation that affected the specimen, before the computer-assisted retrodeformation has been performed; this has also provided the opportunity to reappraise early attempts at restoration. As a result, we offer a revised interpretation for the Ceprano calvarium's original shape, now free from the previous uncertainties, along with insight for its complex depositional and taphonomic history.

Paleomicrobiology of Leprosy.

The use of paleomicrobiological techniques in leprosy has the potential to assist paleopathologists in many important aspects of their studies on the bones of victims, solving at times diagnostic problems. With Mycobacterium leprae, because of the unique nature of the organism, these techniques can help solve problems of differential diagnosis. In cases of co-infection with Mycobacterium tuberculosis, they can also suggest a cause of death and possibly even trace the migratory patterns of people in antiquity, as well as explain changes in the rates and level of infection within populations in antiquity.

Mortality risk factors show similar trends in modern and historic populations exposed to plague.

INTRODUCTION: Plague has been responsible for two major historic pandemics (6th-8th century CE; 14th-19th century CE) and a modern one. The recent Malagasy plague outbreaks raised new concerns on the deadly potential of the plague-causing bacteria Yersinia pestis. Between September 2014 and April 2015, outbreaks of bubonic and pneumonic plague hit the Malagasy population. Two hundred and sixty-three cases, including 71 deaths, have been reported in 16 different districts with a case fatality rate of 27%. The scope of our study was to ascertain whether the risk factors for health in modern-day populations exposed to plague and in ancient populations that faced the two historic pandemics varied or remained substantially unaltered. METHODOLOGY: The risk of mortality of the Malagasy population with those obtained from the reconstruction of three samples of European populations exposed to the historic pandemics was contrasted. RESULTS: The evidence shows that the risks of death are not uniform across age neither in modern nor in historic populations exposed to plague and shows precise concentrations in specific age groups (children between five and nine years of age and young adults). CONCLUSIONS: Although in the post-antibiotic era, the fatality rates have drastically reduced, both modern and historic populations were exposed to the same risk factors that are essentially represented by a low standard of environmental hygiene, poor nutrition, and weak health systems.

A migration-driven model for the historical spread of leprosy in medieval Eastern and Central Europe.

Leprosy was rare in Europe during the Roman period, yet its prevalence increased dramatically in medieval times. We examined human remains, with paleopathological lesions indicative of leprosy, dated to the 6th-11th century AD, from Central and Eastern Europe and Byzantine Anatolia. Analysis of ancient DNA and bacterial cell wall lipid biomarkers revealed Mycobacterium leprae in skeletal remains from 6th-8th century Northern Italy, 7th-11th century Hungary, 8th-9th century Austria, the Slavic Greater Moravian Empire of the 9th-10th century and 8th-10th century Byzantine samples from Northern Anatolia. These data were analyzed alongside findings published by others. M. leprae is an obligate human pathogen that has undergone an evolutionary bottleneck followed by clonal expansion. Therefore M. leprae genotypes and sub-genotypes give information about the human populations they have infected and their migration. Although data are limited, genotyping demonstrates that historical M. leprae from Byzantine Anatolia, Eastern and Central Europe resembles modern strains in Asia Minor rather than the recently characterized historical strains from North West Europe. The westward migration of peoples from Central Asia in the first millennium may have introduced different M. leprae strains into medieval Europe and certainly would have facilitated the spread of any existing leprosy. The subsequent decline of M. leprae in Europe may be due to increased host resistance. However, molecular evidence of historical leprosy and tuberculosis co-infections suggests that death from tuberculosis in leprosy patients was also a factor.

Tuberculosis and leprosy in Italy: new skeletal evidence.

Tuberculosis (TB) and leprosy are infections caused by Mycobacteria. This paper documents new skeletal evidence in Italy from the Iron Age site of Corvaro (Central Italy; 5th century BCE) and the Roman site of Palombara (Central Italy; 4th-5th century CE), and briefly reviews the extant evidence for these infections in Italy. The skeletal evidence for TB in Italy is more ancient than for leprosy, and is more common. The oldest evidence for both mycobacterial diseases is in the North of Italy, but this could be by chance, even if biomolecular models suggest a land route from the East to central Europe, especially for leprosy.

A case of cervical rib andneurovascular compression inRoman period

The possibility to study axial anomalies directly on a skeletal individual is not very frequent. One well preserved skeletal individual from an Italian site dating to the late antique period (5th -4th centuries CE) was studied. This individual shows some interesting skeletal changes in the vertebrae and ribs. A supernumerary rib was found. It is a cervical rib connected to the 1st thoracic rib, presumably with a fibrous bundle. The presence of cervical ribs can produce neurovascular compression of the brachial plexus and subclavian vessels. Because of this, it is often a cause of thoracic out-let syndrome (TOS). In our case the presence of a cervical rib articulated with the first thoracic rib through a probable fibrous band could have re-stricted the space where the brachial plexus and subclavian vessels pass through, creating a state of neurovascular compression, similar

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Biological divergence and equality during the first millennium BC in human populations of central Italy.

The frequencies of nine discrete cranial traits are contrasted among 10 skeletal series of central Italy to assess the patterning of biological affinity or divergence. In this study various statistical applications were used: Mean Measure of Divergence (MMD), which was elaborated using the WPGMA cluster analysis, neighbor-joining method and principal coordinate analysis. The results show two main groups divided by the Apennines, which probably were a geographic barrier to biological exchange during the Italian Iron Age. This fact induced endogamous phenomena in the populations on the two sides of Italy (Adriatic and Tyrrenian) and probably increased the familial segregation of traits. The group on the western side has a further division between samples of the central coast and those of the southern coast. The latter samples seem to be more closely connected to Sardinian peoples, and this indicates gene flow and cultural contacts, which were not hindered by the sea. This segregation appears to have receded by Roman times.