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.

Diet and subsistence in Bronze Age pastoral communities from the southern Russian steppes and the North Caucasus.

The flanks of the Caucasus Mountains and the steppe landscape to their north offered highly productive grasslands for Bronze Age herders and their flocks of sheep, goat, and cattle. While the archaeological evidence points to a largely pastoral lifestyle, knowledge regarding the general composition of human diets and their variation across landscapes and during the different phases of the Bronze Age is still restricted. Human and animal skeletal remains from the burial mounds that dominate the archaeological landscape and their stable isotope compositions are major sources of dietary information. Here, we present stable carbon and nitrogen isotope data of bone collagen of 105 human and 50 animal individuals from the 5th millennium BC to the Sarmatian period, with a strong focus on the Bronze Age and its cultural units including Maykop, Yamnaya, Novotitorovskaya, North Caucasian, Catacomb, post-Catacomb and late Bronze Age groups. The samples comprise all inhumations with sufficient bone preservation from five burial mound sites and a flat grave cemetery as well as subsamples from three further sites. They represent the Caucasus Mountains in the south, the piedmont zone and Kuban steppe with humid steppe and forest vegetation to its north, and more arid regions in the Caspian steppe. The stable isotope compositions of the bone collagen of humans and animals varied across the study area and reflect regional diversity in environmental conditions and diets. The data agree with meat, milk, and/or dairy products from domesticated herbivores, especially from sheep and goats having contributed substantially to human diets, as it is common for a largely pastoral economy. This observation is also in correspondence with the faunal remains observed in the graves and offerings of animals in the mound shells. In addition, foodstuffs with elevated carbon and nitrogen isotope values, such as meat of unweaned animals, fish, or plants, also contributed to human diets, especially among communities living in the more arid landscapes. The regional distinction of the animal and human data with few outliers points to mobility radii that were largely concentrated within the environmental zones in which the respective sites are located. In general, dietary variation among the cultural entities as well as regarding age, sex and archaeologically indicated social status is only weakly reflected. There is, however, some indication for a dietary shift during the Early Bronze Age Maykop period.

Brief communication: paleopathology of the Kiik-Koba 1 Neandertal.

The Kiik-Koba 1 Neandertal partial skeleton (canine, partial hands, partial leg, and feet), of a approximately 40-year-old probable male, exhibits a suite of pathological lesions, including hypercementosis, minor fibrous ossifications, pedal phalangeal fracture, and pronounced enthesopathies on the patella and calcanei in the context of no articular degenerations. The first two sets of lesions are related to age in the context of advanced dental attrition and physical strains. The third lesion joins a series of healed minor traumatic lesions among the Neandertals. The last represents either pronounced tendinous inflammation, albeit in the context of no articular degenerations, or a case of diffuse idiopathic skeletal hyperostosis (DISH) in the Late Pleistocene. Kiik-Koba 1 therefore adds to the high incidence of pathological lesions among the Neandertals and, if a diagnosis of DISH is correct, to a high frequency of this disorder among older Neandertals.

Identification of viral DNA (Anelloviridae) in a 200-year-old dental pulp sample (Napoleon's Great Army, Kaliningrad, 1812).

Ancient human remains are potential sources of biological information including traces of past infections, since previous studies have demonstrated the effective detection of several bacterial agents or host-integrated viruses in old biological remnants like tissues or teeth. Studies of skeletal dental pulp samples are of particular interest since this location is potentially exposed to bloodborne agents during life through its vascularization, and could be considered as well preserved from environment after death of the host. DNA viruses belonging to the family Anelloviridae are highly present in human populations where they harbor an extreme genetic diversity but a yet undefined implication in hosts' health. We hypothesized that anelloviruses would be detected in ancient remains and that they may also serve as tracer viruses for the study of other viral agents. We analyzed 200-year-old dental pulp samples from remains of soldiers of Napoleon's Great Army during the Russian Retreat. Successful detection of Anelloviridae DNA by PCR was obtained for 1/21 ancient samples tested. The sequence identified showed 23% nucleotide divergence with the closest group of modern isolates (genus Gammatorquevirus), and was confirmed as phylogenetically distinct from those identified in saliva samples from the two investigators in charge of the study (genera Alphatorquevirus and Betatorquevirus). PCR directed toward the human beta globin gene was also performed. Negative controls were negative. Our results demonstrate that an ubiquitary, non-integrated, DNA virus is detectable from ancient biological material, with potential developments in terms of evolution studies or subsequent molecular investigations involving further viral agents.

The environment and health condition of the upper palaeolithic sunghir people of Russia.

Human bones from the Sunghir Late Palaeolithic settlement of the Northern-East part of the Eastern European Plane were observed by a gross study of possible skeletal lesions. The complex of pathological conditions we studied could mirror the features of the ancient environment. The climatic conditions of the Upper Palaeolithic, especially in its final stages, were severe. Thus environmental change and the fall of temperature is reflected in the distribution of pathological indicators. The comparative analysis of early and late Upper Palaeolithic populations demonstrates the increasing frequency of some stress markers. The analysis of physiological stress markers convincingly demonstrates that the Sunghir people had an active lifestyle without experiencing considerable negative stress. Living in the cold conditions and a humid climate, the Sunghir people had adequate reactions relative to their life conditions. Different types of physical activity were noted for both children and adult man. It could be that this is the result of the influence of gender diversity in labour.

Double child burial from Sunghir (Russia): pathology and inferences for upper paleolithic funerary practices.

The double child burial from Sunghir (Russia) is a spectacular Mid Upper Palaeolithic funerary example dated to about 24,000 BP. A boy (Sunghir 2) and a girl (Sunghir 3), about 12-13 and 9-10 years old, respectively, were buried at the same time, head to head, covered by red ocher and ornamented with extraordinarily rich grave goods. Examination of the two skeletons reveals that the Sunghir 3 femora are short and exhibit marked antero-posterior bowing. The two femora do not show any asymmetry in the degree of shortening and bowing. Bowing affects the whole diaphysis and shows a regularly incurved profile, with the highest point at midshaft. Pathology is confined to the femora, and no other part of this well-preserved specimen shows abnormality. The isolated nature of the Sunghir 3 anomalies points to cases reported in the medical literature under the label of "congenital bowing of long bones" (CBLB). These are a group of rare conditions exhibiting localized, sometimes bilateral, bowing and shortening which are nonspecific and may result from different causes, including abnormalities of the primary cartilaginous anlage (i.e., the aggregation of cells representing the first trace of an organ). Localized ossification disturbances, possibly linked to a diabetic maternal condition, might explain the shortening and the coincidence of maximum midshaft curvature with the position of the primary ossification center, as well as the lack of involvement of other skeletal parts. This scenario, rather than other possibilities (early bilateral midshaft fracture, acute plastic bowing deformities, or faulty fetal posture), provides the most likely explanation for the Sunghir 3 femoral deformities. The intriguing combination of a pathological condition apparent since birth with a spectacular burial of unusually positioned young individuals of different sexes recalls significant aspects of the triple burial from the contemporary site of Dolní Vestonice (Moravia), evoking a patterned relationship between physical abnormality and extraordinary Upper Paleolithic funerary behavior.