Assessing autosomal aneuploidy in ancient genomes.

Using genetic methods, aneuploidies can be detected in ancient human remains, which is so far the only way to reliably prove their existence in the past. As highlighted in recent studies by Rohrlach et al. and by Anastasiadou et al., this initial step enables a deeper exploration of the history of rare diseases, encompassing the social and historical contexts of the afflicted individuals.

Pathogen prospecting of museums: Reconstructing malaria epidemiology.

Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.

Histological analysis and etiology of a pathological iguanodontian femur from England.

Derived ornithopods, such as hadrosaurids, show a high occurrence of fossilized lesions and diseases. However, paleopathologies in iguanodontians seem to be less common, considering the rich fossil record of these taxa in Europe, in particular in Belgium, Britain and Spain. Here, we describe an iguanodontian femur discovered in England that exhibits a large overgrowth of its lateral aspect, not previously recognized in any other similar remains. The specimen was scanned with micro-computed tomography (microCT) and later sectioned in three sites of the overgrowth for histological analysis. The femur belongs to an early adult Iguanodontia indet., based on the presence of a woven parallel fibered complex in the outer cortex and three to four lines of arrested growth. Internal analysis of the dome-like overgrowth suggests it can be diagnosed as a fracture callus. The injury might have negatively impacted upon the animal's locomotion as the trauma had occurred in the region above the knee, a crucial spot for hindlimb musculature. Finally, a cancellous medullary bone-like tissue was recognized in the medullary cavity next to the pathological overgrowth. An attempt was made to determine the precise nature of this tissue, as medullary bone is linked with the ovulation period in (avian) dinosaurs, whereas other types of endosteal, medullary bone-like tissue have previously been recognized in pathological bones.

Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens.

The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.

Preservation of the heart in ancient Egyptian mummies: A computed tomography investigation with focus on the myocardium.

The ancient Egyptians considered the heart to be the most important organ. The belief that the heart remained in the body is widespread in the archeological and paleopathological literature. The purpose of this study was to perform an overview of the preserved intrathoracic structures and thoracic and abdominal cavity filling, and to determine the prevalence and computed tomography (CT) characteristics of the myocardium in the preserved hearts of ancient Egyptian mummies. Whole-body CT examinations of 45 ancient Egyptian mummies (23 mummies from the Ägyptisches Museum und Papyrussammlung, Berlin, Germany, and 22 mummies from the Museo Egizio, Turin, Italy) were systematically assessed for preserved intrathoracic soft tissues including various anatomical components of the heart (pericardium, interventricular septum, four chambers, myocardium, valves). Additionally, evidence of evisceration and cavity filling was documented. In cases with identifiable myocardium, quantitative (measurements of thickness and density) and qualitative (description of the structure) assessment of the myocardial tissue was carried out. Heart structure was identified in 28 mummies (62%). In 33 mummies, CT findings demonstrated evisceration, with subsequent cavity filling in all but one case. Preserved myocardium was identified in nine mummies (five male, four female) as a mostly homogeneous, shrunken structure. The posterior wall of the myocardium had a mean maximum thickness of 3.6 mm (range 1.4-6.6 mm) and a mean minimum thickness of 1.0 mm (range 0.5-1.7 mm). The mean Hounsfield units (HU) of the myocardium at the posterior wall was 61 (range, 185-305). There was a strong correlation between the HU of the posterior wall of the myocardium and the mean HU of the muscles at the dorsal humerus (R = 0.77; p = 0.02). In two cases, there were postmortem changes in the myocardium, most probably due to insect infestation. To our knowledge, this is the first study to investigate the myocardium systematically on CT scans of ancient Egyptian mummies. Strong correlations between the densities of the myocardium and skeletal muscle indicated similar postmortem changes of the respective musculature during the mummification process within individual mummies. The distinct postmortem shrinking of the myocardium and the collapse of the left ventriclular cavity in several cases did not allow for paleopathological diagnoses such as myocardial scarring.

Three-dimensional reconstruction of King Henri IV's paranasal sinuses and mastoid cells.

PURPOSE: The preserved head of King Henri IV of France (life 1553-1610, reign 1589-1610) has survived to the present day thanks to high-quality embalming and favorable conservation conditions. The aim of this study was to examine Henry IV's upper resonant cavities and mastoids using an original and innovative forensic three-dimensional segmentation method. METHODS: The paranasal sinuses and mastoid cells of King Henri IV of France were studied by cross-referencing available biographical information with clinical and flexible endoscopic examination and computed tomography (CT-scan) imaging. The paranasal sinuses and mastoid cells were delineated and their volumes were assessed using ITK-SNAP 4.0 software (open-source). Graphical representations were created using Fusion 360® (Autodesk Inc., San Rafael, CA, USA) and MeshMixer® (Autodesk Inc., San Rafael, CA, USA). RESULTS: Paranasal sinus tomodensitometry revealed abnormalities in shape and number. Henri IV of France suffered from sinus aplasia. Neither the left sphenoid nor left frontal sinus contrasted sharply, and a remarkable pneumatization of the right clinoid processes extended throughout the height of the right pterygoid process. The total volumes of Henri IV's mastoid air-cells were estimated at 27 and 26 mL, respectively, for the right and left sides, exceeding the normal mean and the maximum of modern subjects by a wide margin. No sign of chronic ear or sinus condition was found. CONCLUSIONS: An innovative method has been developed in forensic medicine to establish hypotheses about the growth and respiratory conditions of the face.

A Case of Acute Plastic Deformation of the Forearm in a Medieval Hispano-Mudejar Skeleton (13-14th Centuries AD).

INTRODUCTION: Acute plastic deformation refers to a traumatic bending or bowing without a detectable cortical defect. CASE PRESENTATION AND DISCUSSION: We describe a rare case from an individual that was exhumed from the Hispano-Mudejar necropolis in Uceda (Guadalajara, Spain) dated between the 13th and 14th centuries AD. The case corresponds to an adult woman, with a bowing involvement of the left ulna and radius. After making the differential diagnosis with various pathologies likely to present with this alteration, we reached the diagnosis of acute plastic deformation of the forearm through external and radiological examination and comparison with the healthy contralateral forearm. CONCLUSIONS: Acute plastic deformation is a rare traumatic injury, not described until the last century and only rarely described in palaeopathological contexts. We contribute a new case, the first being sufficiently documented, contributing to the knowledge and diagnosis of this type of trauma in the ancient bone, while deepening the knowledge of the living conditions of the medieval Mudejar population of Uceda.

The Friar with the Crutch: A Pictorial Hint of the Stroke Suffered by Bernardino da Fossa (1420-1503).

BACKGROUND: Works of art may serve as a source of evidence of diseases and help to better understand their natural history. SUMMARY: Bernardino da Fossa was a 15th-century Italian Franciscan friar who wrote sermons and historical works. He described the events of the Observance Reformation movement since its dawn, but the last chapter is unexplainably interrupted. This has been considered suggestive for an acute and disabling illness. A painting dating back 12 years after his death depicts Bernardino holding a crutch with his left arm. This may represent an important clue to establish a gait disturbance, whereas the permanent interruption in drafting his writing may be ascribed to a serious writing impairment. KEY MESSAGES: The historical detail of the writing suspension and the crutch in this painting represent important hints of the stroke suffered by Bernardino da Fossa.

Deep Paleoproteotyping and Microtomography Revealed No Heart Defect nor Traces of Embalming in the Cardiac Relics of Blessed Pauline Jaricot.

Scientific examination of the heart of Blessed Pauline Jaricot-a French missionary figure-was carried out in 2022. As tandem mass spectrometry proteotyping has proven to be valuable to obtain the broad taxonomic repertoire of a given sample without any a priori information, we aimed at exploring the conditions of preservation of the relics and possible conditions of death. Metaproteomics and high-resolution microtomography imaging approaches were combined. A dataset comprising 6731 high-resolution MS/MS spectra was acquired and 968 of these spectra could be assigned to specific peptidic biomolecules. Based on the taxonomical information encompassed by the identified peptide sequences, 5 phyla were identified amongst eukaryota (94% of the biomass): Ascomycota (55%), with the species Aspergillus versicolor, Trichophyton mentagrophytes and Aspergillus glaucus, corresponding to expected cadaverous fungal flora; Chordata (42%), represented by a unique species, Homo sapiens; Streptophyta (3%); and Arthropoda (traces). Bacteria (6% of the biomass) were poorly represented. No trace of embalming substance could be retrieved, nor any pathogens. Imaging evidenced no heart defect nor embalming traces. No evidence that was inconsistent with natural and spontaneous conservation could be retrieved. This study prefigures the power of modern molecular techniques such as paleoproteotyping coupled to microtomography to gain insight into historical relics.

Genomics of Ancient Pathogens: First Advances and Prospects.

Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today's world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersinia pestis (plague), Variola virus (smallpox), Vibrio cholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy), and Treponema pallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history.

Ankylosing spondylitis on unidentified individual from early modern times found in reformed church (Silická Brezová, Slovakia): a case-based review.

The grave situated in the central part of the reformed church in Silická Brezová in Slovakia contained the human skeletal remains of one individual. The aim of this study was to confirm the presence of ankylosing spondylitis on these skeletal remains. Determine the sex, age at death, stature, and ancestry of the individual by anthropological methods, and also record and identify other pathological manifestations of diseases. A macroscopic examination has been carried out, with the analysis of the palaeopathological conditions of the remains, and subsequently an X-ray and CT completed analysis. The skeleton belonged to a male of European origin, aged between 45 and 60 years at the time of death. Stature calculated from the maximal length of his femur was 163.12 ± 3.48 cm. Pathological features were identified on the many bones. Ankylosis affected almost the whole spinal cord, including the sacroiliac joints. The skeleton also presented the manifestation of many entheseal changes. Presence of the ankylosing spondylitis was confirmed by a combination of standard anthropological methods and modern diagnostic methods (X-ray and CT analysis). It is a specific disease with a prevalence between 0.1 and 1% worldwide. There is a potential for further genetic research to determine the degree of genetic relatedness with an individual living in this village who has been diagnosed with the same disease.

Morphology, pathology, and the vertebral posture of the La Chapelle-aux-Saints Neandertal.

Although the early postural reconstructions of the Neandertals as incompletely erect were rejected half a century ago, recent studies of Neandertal vertebral remains have inferred a hypolordotic, flat lower back and spinal imbalance for them, including the La Chapelle-aux-Saints 1 skeleton. These studies form part of a persistent trend to view the Neandertals as less "human" than ourselves despite growing evidence for little if any differences in basic functional anatomy and behavioral capabilities. We have therefore reassessed the spinal posture of La Chapelle-aux-Saints 1 using a new pelvic reconstruction to infer lumbar lordosis, interarticulation of lower lumbar (L4-S1) and cervical (C4-T2) vertebrae, and consideration of his widespread age-related osteoarthritis. La Chapelle-aux-Saints 1 exhibits a pelvic incidence (and hence lumbar lordosis) similar to modern humans, articulation of lumbar and cervical vertebrae indicating pronounced lordosis, and Baastrup disease as a product of his advanced age, osteoarthritis, and lordosis. Our findings challenge the view of generally small spinal curvatures in Neandertals. Setting aside the developmentally abnormal Kebara 2 vertebral column, La Chapelle-aux-Saints 1 is joined by other Neandertals with sufficient vertebral remains in providing them with a fully upright (and human) axial posture.

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.

Multidisciplinary investigation of an ancient renal stone in a mummy from Popoli, central Italy.

The renal stone found in the natural mummy of an anonymous nobleman dating to 19th century was investigated using advanced imaging modalities and analytic investigations. By this multidisciplinary approach we were able to identify the chemical components and their distribution throughout the sample. These results allowed to understand the lifestyle habits of the subject, as well as the exact pathogenesis of his disease.

The "Queen of the Moors". Paleopathological investigation of a natural mummy from Scicli, South-Eastern Sicily.

A natural, well-preserved mummy belonging to a 45-55 year old female was found in the Church of Santa Maria della Consolazione in Scicli, south-eastern Sicily. The body was submitted to external examination, digital radiology, and computed tomography scanning. Paleopathological investigation allowed us to detect pulmonary pathology related to tuberculosis, atherosclerosis, and phleboliths. The presence of the latter, along with good dental condition with focal caries and obesity indicates a subject belonging to a high social class in good nutritional status. Along with other examples, this case allows to infer that tuberculosis was a common disease in that area, if not in the whole island, prior to the antibiotic era. Mummies need to be properly surveyed and protected, but also adequately studied by multidisciplinary teams of experts. The presence in such a team of at least one skilled anatomic/surgical pathologist, as long as well trained in the study of ancient human remains, represents an undeniable condition.

Using a multimethod life history approach to navigate the osteological paradox: A case study from Prehispanic Nasca, Peru.

OBJECTIVES: We leverage recent bioarchaeological approaches and life history theory to address the implications of the osteological paradox in a study population. The goal of this article is to evaluate morbidity and mortality patterns as well as variability in the risk of disease and death during the Late Intermediate period (LIP; 950-1450 C.E.) in the Nasca highlands of Peru. We demonstrate how the concurrent use of multiple analytical techniques and life history theory can engage the osteological paradox and provide salient insights into the study of stress, frailty, and resilience in past populations. MATERIALS AND METHODS: Crania from LIP burial contexts in the Nasca highlands were examined for cribra orbitalia (n = 325) and porotic hyperostosis (n = 270). All age groups and both sexes are represented in the sample. Survivor/nonsurvivor analysis assessed demographic differences in lesion frequency and severity. Hazard models were generated to assess differences in survivorship. The relationship between dietary diversity and heterogeneity in morbidity was assessed using stable δ15 N and δ13 C isotope values for bone collagen and carbonate. One hundred and twenty-four crania were directly AMS radiocarbon dated, allowing for a diachronic analysis of morbidity and mortality. RESULTS: The frequency and expression of both orbital and vault lesions increases significantly during the LIP. Survivor/nonsurvivor analysis indicates cranial lesions co-vary with frailty rather than robusticity or longevity. Hazard models show (1) decreasing survivorship with the transition into the LIP, (2) significantly lower adult life expectancy for females compared to males, and (3) individuals with cranial lesions have lower survivorship across the life course. Stable isotope results show very little dietary diversity. Mortality risk and frequency of pathological skeletal lesions were highest during Phase III (1300-1450 C.E.) of the LIP. CONCLUSION: Results provide compelling evidence of increasing physiological stress and mortality in the Nasca highlands during the LIP, but also reveal substantial heterogeneity in frailty and the risk of death. Certain members of society experienced a heavier disease burden and higher mortality compared to their contemporaries. Elevated levels of disease and lethal trauma among females account for some of the sex differences in survivorship but cannot explain the large degree of female-biased mortality. We hypothesize that parental investment in males or increased female fertility rates may explain these differences.

An image analysis protocol for the quantification of interglobular dentine in anthropological tooth sections.

The histological identification of interglobular dentine (IGD) in archeological human remains with macroscopic evidence of rickets has opened a promising new avenue for the investigation of metabolic disease in the past. Recent paleopathological studies have shown that histological analysis of archeological human teeth may allow the identification of periods of vitamin D deficiency occurring within very narrow developmental windows, yielding new information on the seasonality or even maternal-fetal transmission of this disease. However, currently available techniques for recording IGD rely on subjective scoring systems or visual estimations, potentially leaving them open to inter and intra-observer error and rendering comparisons of datasets difficult. Here we describe a new imaging protocol that utilizes open access software and may yield more objective and quantitative data on the amount of IGD present within a dentinal region of interest. We demonstrate that grayscale histograms in FIJI®/ImageJ® might be used to provide less subjective estimates of the percentage of a region of interest affected by IGD. Application of this technique may enable more accurate comparison of datasets between researchers.

Toward a bioarchaeology of urbanization: Demography, health, and behavior in cities in the past.

Urbanization is one of the most important settlement shifts in human history and has been the focus of research within bioarchaeology for decades. However, there have been limited attempts to synthesize the results of these studies in order to gain a broader perspective on whether or how urbanization affects the biology, demography, and behavior of humans, and how these potential effects are embodied in the human skeleton. This paper outlines how bioarchaeology is well-suited to examine urbanization in the past, and we provide an overview and examples of three main ways in which urbanization is studied in bioarchaeological research: comparison of (often contemporaneous) urban and rural sites, synchronic studies of the variation that exists within and between urban sites, and investigations of changes that occur within urban sites over time. Studies of urbanization, both within bioarchaeology and in other fields of study, face a number of limitations, including a lack of a consensus regarding what urban and urbanization mean, the assumed dichotomous nature of urban versus rural settlements, the supposition that urbanization is universally bad for people, and the assumption (at least in practice) of homogeneity within urban and rural populations. Bioarchaeologists can address these limitations by utilizing a wide array of data and methods, and the studies described here collectively demonstrate the complex, nuanced, and highly variable effects of urbanization.

Quantifying cortical bone in fragmentary archeological second metacarpals.

OBJECTIVES: Skeletal variation in cortical bone thickness is an indicator of bone quality and health in archeological populations. Second metacarpal radiogrammetry, which measures cortical thickness at the shaft midpoint, is traditionally used to evaluate bone loss in bioarcheological and some clinical contexts. However fragmentary elements are regularly omitted because the midpoint cannot be determined. This methodological limitation reduces sample sizes and biases them against individuals prone to fracture, such as older individuals with low bone mass. This study introduces a new technique for measuring cortical bone in second metacarpals, the "Region of Interest" (ROI) method, which quantifies bone in archeological remains with less-than-ideal preservation while accounting for cortical heterogeneity. MATERIALS AND METHODS: The ROI method was adapted from digital X-ray radiogrammetry (DXR), a clinical method used to estimate bone mineral density, and tested using second metacarpals from Middenbeemster, Netherlands, a 19th century known age and sex skeletal collection. The ROI method quantifies cortical bone area within a 1.9 cm-long, mid-diaphyseal region, standardized for body size differences using total area (CAIROI ). CAIROI values were compared to traditional radiogrammetric cortical indices (CI) to assess the method's ability to identify age-related bone loss. RESULTS: CAIROI values have high intra- and interobserver replicability and are strongly and significantly correlated with CI values for both males (r[n = 39] = 0.906, p = 0.000) and females (r[n = 58] = 0.925, p = 0.000). CONCLUSION: The ROI method complements traditional radiogrammetry analyses and provides a reliable way to quantify cortical bone in incomplete second metacarpals, thereby maximizing sample sizes, allowing patterns in bone acquisition and loss to be more comprehensively depicted in archeological assemblages.

An abundance of developmental anomalies and abnormalities in Pleistocene people.

Diverse developmental abnormalities and anomalous features are evident in the Pleistocene Homo fossil record, varying from minor but rare dental, vertebral, and carpal variants to exceptional systemic disorders. There are currently 75 documented anomalies or abnormalities from 66 individuals, spanning the Pleistocene but primarily from the Late Pleistocene Middle and Upper Paleolithic with their more complete skeletal remains. The expected probabilities of finding these variants or developmental disorders vary from <5% to <0.0001%, based on either recent human incidences or relevant Pleistocene sample distributions. Given the modest sample sizes available for the skeletal or dental elements in question, especially if the samples are appropriately limited in time and geography, the cumulative multiplicative probability of finding these developmental changes is vanishingly small. These data raise questions regarding social survival abilities, differing mortuary treatments of the biologically unusual, the role of ubiquitous stress among these Pleistocene foragers, and their levels of consanguinity. No single factor sufficiently accounts for the elevated level of these developmental variants or the low probability of finding them in the available paleontological record.