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The detection of parasite infections in past populations has classically relied on microscopic analysis of sediment samples and coprolites. In recent years, additional methods have been integrated into paleoparasitology such as enzyme-linked immunosorbent assay (ELISA) and ancient DNA (aDNA). The aim of this study was to evaluate a multimethod approach for paleoparasitology using microscopy, ELISA, and sedimentary ancient DNA (sedaDNA) with a parasite-specific targeted capture approach and high-throughput sequencing. Using 26 samples dating from c. 6400 BCE to 1500 CE that were previously analyzed with microscopy and ELISA, we aimed to more accurately detect and reconstruct parasite diversity in the Roman Empire and compare this diversity to earlier and later time periods to explore temporal changes in parasite diversity. Microscopy was found to be the most effective technique for identifying the eggs of helminths, with 8 taxa identified. ELISA was the most sensitive for detecting protozoa that cause diarrhea (notably Giardia duodenalis ). Parasite DNA was recovered from 9 samples, with no parasite DNA recovered from any pre-Roman sites. Sedimentary DNA analysis identified whipworm at a site where only roundworm was visible on microscopy, and also revealed that the whipworm eggs at another site came from two different species ( Trichuris trichiura and Trichuris muris ). Our results show that a multimethod approach provides the most comprehensive reconstruction of parasite diversity in past populations. In the pre-Roman period, taxonomic diversity included a mixed spectrum of zoonotic parasites, together with whipworm, which is spread by ineffective sanitation. We see a marked change during the Roman and medieval periods with an increasing dominance of parasites transmitted by ineffective sanitation, especially roundworm, whipworm and protozoa that cause diarrheal illness.

Zoonoses are among the greatest threats to human health, with many zoonotic pathogens believed to have emerged following the Neolithic transition. Palaeomicrobiological investigations of the zooarchaeological record hold potential to uncover the reservoirs, host ranges, and host adaptations of zoonotic pathogens in the past, but face challenges in identifying promising specimens and pathogen DNA preservation. We perform palaeopathological and genetic examinations of 346 skeletal elements from domesticated and wild animals collected from 34 Eurasian sites dating across the last six millennia. We identify 116 signatures of 29 ancient (opportunistic) pathogens and find support that palaeopathological lesions provide guidance for specimen selection. For two pathogen species, Erysipelothrix rhusiopathiae and Streptococcus lutetiensis , we confirm their ancient authenticity using phylogenetics, showcasing an approach to explore the relationship between ancient low-coverage genomes and their modern-day relatives. Our work presents a pathway to understanding prehistoric zoonotic diseases by integrating zooarchaeological, palaeopathological, and genetic data. Authors investigate ancient DNA from animal remains and identify multiple signatures of ancient zoonotic pathogens. They find ancient pathogen genomics from archaeological animal remains may inform zoonotic disease emergence.

Dental calculus is a microbial biofilm that contains biomolecules from oral commensals and pathogens, including those potentially related to cause of death (CoD). To assess the utility of calculus as a diagnostically informative substrate, in conjunction with paleopathological analysis, calculus samples from 39 individuals in the Smithsonian Institution’s Robert J. Terry Collection with CoDs of either syphilis or tuberculosis were assessed via shotgun metagenomic sequencing for the presence of Treponema pallidum subsp . pallidum and Mycobacterium tuberculosis complex (MTBC) DNA. Paleopathological analysis revealed that frequencies of skeletal lesions associated with these diseases were partially inconsistent with diagnostic criteria. Although recovery of T. p. pallidum DNA from individuals with a syphilis CoD was elusive, MTBC DNA was identified in at least one individual with a tuberculosis CoD. The authenticity of MTBC DNA was confirmed using targeted quantitative PCR assays, MTBC genome enrichment, and in silico bioinformatic analyses; however, the lineage of the MTBC strain present could not be determined. Overall, our study highlights the utility of dental calculus for molecular detection of tuberculosis in the archaeological record and underscores the effect of museum preparation techniques and extensive handling on pathogen DNA preservation in skeletal collections.

Mass graves are usually key historical markers with strong incentive for archeological investigations. The identification of individuals buried in mass graves has long benefitted from traditional historical, archaeological, anthropological and paleopathological techniques. The addition of novel methods including genetic, genomic and isotopic geochemistry have renewed interest in solving unidentified mass graves. In this study, we demonstrate that the combined use of these techniques allows the identification of the individuals found in two Breton historical mass graves, where one method alone would not have revealed the importance of this discovery. The skeletons likely belong to soldiers from the two enemy armies who fought during a major event of Breton history: the siege of Rennes in 1491, which ended by the wedding of the Duchess of Brittany with the King of France and signaled the end of the independence of the region. Our study highlights the value of interdisciplinary approaches with a particular emphasis on increasingly accurate isotopic markers. The development of the sulfur isoscape and testing of the triple isotope geographic assignment are detailed in a companion paper [13].

At the Abony-Turjányos dűlő site, located in Central Hungary, a rescue excavation was carried out. More than 400 features were excavated and dated to the Protoboleráz horizon, at the beginning of the Late Copper Age in the Carpathian Basin, between 3780-3650 cal BC. Besides the domestic and economic units, there were two special areas, with nine-nine pits that differed from the other archaeological features of the site. In the northern pit group seven pits contained human remains belonging to 48 individuals. Some of them were buried carefully, while others were thrown into the pits. The aim of this study is to present the results of the paleopathological and molecular analysis of human remains from this Late Copper Age site. The ratio of neonates to adults was high, 33.3%. Examination of the skeletons revealed a large number of pathological cases, enabling reconstruction of the health profile of the buried individuals. Based on the appearance and frequency of healed ante- and peri mortem trauma, inter-personal (intra-group) violence was characteristic in the Abony Late Copper Age population. However other traces of paleopathology were observed on the bones that appear not to have been caused by warfare or inter-group violence. The remains of one individual demonstrated a rare set of bone lesions that indicate the possible presence of leprosy (Hansen's disease). The most characteristic lesions occurred on the bones of the face, including erosion of the nasal aperture, atrophy of the anterior nasal spine, inflammation of the nasal bone and porosity on both the maxilla and the bones of the lower legs. In a further four cases, leprosy infection is suspected but other infections cannot be excluded. The morphologically diagnosed possible leprosy case significantly modifies our knowledge about the timescale and geographic spread of this specific infectious disease. However, it is not possible to determine the potential connections between the cases of possible leprosy and the special burial circumstances.

Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it initially intended to interpret migration, evolution, and dispersion patterns of ancient parasites, along with their hosts. Recently, paleoparasitology has been used to better understand dietary habits and lifestyles of ancient human societies. Paleoparasitology is increasingly being recognized as an interdisciplinary field within paleopathology that integrates areas such as palynology, archaeobotany, and zooarchaeology. Paleoparasitology also incorporates techniques such as microscopy, immunoassays, PCR, targeted sequencing, and more recently, high-throughput sequencing or shotgun metagenomics to understand ancient parasitic infections and thus interpret migration and evolution patterns, as well as dietary habits and lifestyles. The present review covers the original theories developed in the field of paleoparasitology, as well as the biology of some parasites identified in pre-Columbian cultures. Conclusions, as well as assumptions made during the discovery of the parasites in ancient samples, and how their identification may aid in better understanding part of human history, ancient diet, and lifestyles are discussed.

In 2001, a nearly complete sub-adult Tenontosaurus tilletti was collected from the Antlers Formation (Aptian-Albian) of southeastern Oklahoma. Beyond its exceptional preservation, computed tomography (CT) and physical examination revealed this specimen has five pathological elements with four of the pathologies a result of trauma. Left pedal phalanx I-1 and left dorsal rib 10 are both fractured with extensive callus formation in the later stages of healing. Left dorsal rib 7 (L7) and right dorsal rib 10 (R10) exhibit impacted fractures compressed 26 mm and 24 mm, respectively. The fracture morphologies in L7 and R10 indicate this animal suffered a strong compressive force coincident with the long axis of the ribs. All three rib pathologies and the pathological left phalanx I-1 are consistent with injuries sustained in a fall. However, it is clear from the healing exhibited by these fractures that this individual survived the fall. In addition to traumatic fractures, left dorsal rib 10 and possibly left phalanx I-1 have a morphology consistent with post-traumatic infection in the form of osteomyelitis. The CT scans of left metacarpal IV revealed the presence of an abscess within the medullary cavity consistent with a subacute form of hematogenous osteomyelitis termed a Brodie abscess. This is only the second reported Brodie abscess in non-avian dinosaurs and the first documented occurrence in herbivorous dinosaurs. The presence of a Brodie abscess, known only in mammalian pathological literature, suggest mammalian descriptors for bone infection may be applicable to non-avian dinosaurs.

The field of ancient DNA (aDNA) has rapidly accelerated in recent years as a result of new methods in next-generation sequencing, library preparation and targeted enrichment. Such research is restricted, however, by the highly variable DNA preservation within different tissues, especially when isolating ancient pathogens from human remains. Identifying positive candidate samples via quantitative PCR (qPCR) for downstream procedures can reduce reagent costs, increase capture efficiency and maximize the number of sequencing reads of the target. This study uses four qPCR assays designed to target regions within the Mycobacterium tuberculosis complex (MTBC) to examine 133 human skeletal samples from a wide geographical and temporal range, identified by the presence of skeletal lesions typical of chronic disseminated tuberculosis. Given the inherent challenges working with ancient mycobacteria, strict criteria must be used and primer/probe design continually re-evaluated as new data from bacteria become available. Seven samples tested positive for multiple MTBC loci, supporting them as strong candidates for downstream analyses. Using strict and conservative criteria, qPCR remains a fast and effective screening tool when compared with screening by more expensive sequencing and enrichment technologies.

Seventy-one individuals from the late Neolithic population of the 7000-year-old site of Hódmezővásárhely-Gorzsa were examined for their skeletal palaeopathology. This revealed numerous cases of infections and non-specific stress indicators in juveniles and adults, metabolic diseases in juveniles, and evidence of trauma and mechanical changes in adults. Several cases showed potential signs of tuberculosis, particularly the remains of the individual HGO-53. This is an important finding that has significant implications for our understanding of this community. The aim of the present study was to seek biomolecular evidence to confirm this diagnosis. HGO-53 was a young male with a striking case of hypertrophic pulmonary osteopathy (HPO), revealing rib changes and cavitations in the vertebral bodies. The initial macroscopic diagnosis of HPO secondary to tuberculosis was confirmed by analysis of Mycobacterium tuberculosis complex specific cell wall lipid biomarkers and corroborated by ancient DNA (aDNA) analysis. This case is the earliest known classical case of HPO on an adult human skeleton and is one of the oldest palaeopathological and palaeomicrobiological tuberculosis cases to date.

Paleopathological assessment of the late Middle Pleistocene archaic human cranium from Maba, South China, has documented a right frontal squamous exocranially concave and ridged lesion with endocranial protrusion. Differential diagnosis indicates that it resulted from localized blunt force trauma, due to an accident or, more probably, interhuman aggression. As such it joins a small sample of pre-last glacial maximum Pleistocene human remains with probable evidence of humanly induced trauma. Its remodeled condition also indicates survival of a serious pathological condition, a circumstance that is increasingly documented for archaic and modern Homo through the Pleistocene.