Ancient genome analysis has become an indispensable tool in studies of human population history and evolution since the breakthrough of whole-genome sequencing technology. The problem remains, however, that ancient genomes cannot be analyzed without crushing non-small pieces of precious specimens; moreover, in many cases, there is insufficient DNA remaining in the pieces of sample to obtain whole-genome sequences. In previous studies, therefore, a couple of indicators (e.g. racemization ratios) have been proposed to estimate the endogenous DNA in ancient samples. However, these studies have used polymerase chain reaction (PCR) to test whether endogenous DNA remains, but this has proved inadequate because the success or failure of PCR amplification does not necessarily reflect the DNA remaining. To assess the amount of endogenous DNA, we use the ratios of reads generated by next-generation sequencing (NGS) mapped to the human reference genome sequence. We investigated 40 human remains excavated from three shell-mound sites of the late to final Jomon culture. The associations between the environmental/molecular factors and the mapping ratios (MRs) were examined. There were no significant associations between the environmental factors and MRs, or between the collagen residual ratios (CRRs) and the MRs. However, we found a significant association between CRRs in rib bones and MRs. The weight of bone required to measure residual collagen is much less than that required to obtain the DNA necessary for NGS analysis, and the process of measuring CRRs is always involved in dating. Hence, we propose the collagen in the ribs as a good indicator for successful ancient genome analyses.

This article describes the skeletal remains of a 20th-century individual diagnosed with poliomyelitis in childhood who suffered from atrophy and muscle weakness as an adult. The study provides a detailed analysis of both the primary effects of polio in the skeleton and the secondary effects across a lifetime, and contributes to the future identification of this pathology in osteoarchaeological assemblages. A skeleton of an 82-year-old male with poliomyelitis, from Tierra de la Reina, León (Spain) was submitted to bone densitometry, morphological, metric, cross-sectional, and palaeopathological analyses. Conventional X-rays and computed tomography scans were also performed. Skeletal alterations were categorized as directly and indirectly related to polio. The latter were probably acquired during life, resulting from mobility problems, malposition, and/or advanced age. Discrepancies in size, primarily related to polio, were observed between the right and left sides of the skeleton, with the left side being smaller and more gracile. However, while the asymmetry of the upper limbs is mainly in robustness, in the lower limbs the differences are in both robustness and length. This paper illustrates the skeletal alterations that may be present with poliomyelitis, demonstrating the complexity of diagnosing this pathology in an individual who lived a long life. In fact, many of the observed alterations can be found in other pathological conditions. Therefore, it is concluded that extreme caution be taken when analysing archaeological skeletal remains that are not as complete and well-preserved as this individual. The present work contributes to the diagnosis of poliomyelitis in human remains and underscores its impact in human history. Destructive methods were not authorized; medical records were no longer available. In the future, 3D reconstruction analysis/micro-computed tomography may add new and valuable information.

This study describes a non-adult individual with bone features suggestive of β-thalassemia, a disease commonly found in malaria-endemic regions today and in the past. The skeleton of a 5.5- to 6.5-year-old child exhumed from a 16th- to 18th-century CE necropolis in Almeirim (Portugal) was examined macroscopically, with a scanning electron microscope, and by conventional radiology and computed tomography. This individual shows frontoparietal diploic hyperplasia with a slight hair-on-end radiographic appearance and an exuberant serpiginous pattern. The orbital roofs have a plaque-like formation and facial bones display new bone proliferation and porosity. The teeth show caries, calculus deposition, anomalies on the four deciduous canine roots, and linear enamel hypoplasia on the first permanent right upper central incisor. The postcranial skeleton presents osteopenic trabecular appearances, cribra humeralis, and cribra femoralis, the latter associated with malaria. A second non-adult individual (2.5–3.5 years old) had similar lesions in the cranium, raising the question of whether they were siblings. The lesions are consistent with β-thalassemia intermedia, a homozygous or compound heterozygous hemoglobinopathy found in malaria-endemic regions, such as Almeirim, due to the protective advantage conferred by β-thalassemia carriers. Thalassemia presents a wide spectrum of lesions common in other hemolytic anemias, which makes the diagnosis a challenge. Hopefully, biomolecular techniques will assist the diagnosis in skeletonized individuals. To the authors’ knowledge, this is the first possible case of thalassemia in the westernmost part of Europe, in a region currently with high prevalence of hemoglobinopathies, attributed to the past Islamic and sub-Saharan presence, and in an area historically affected by malaria.

Previous bioarchaeological and auxological research has indicated that stunting the growth of vertebral measures, specifically those of the vertebral neural canal (VNC), provides a record of stressful early-childhood episodes that persists into adulthood. The main goal of this study was to investigate possible VNC size variation within the specific context of a medieval silver-mining site. Skeletons unearthed recently at Kutná Hora–Sedlec (Czech Republic) represent a population that lived there during its most prosperous era (13th–16th centuries). During this period, Kutná Hora residents could have faced both environmental and cultural conditioned stressors. In a total of 207 individuals examined in this study, we measured anteroposterior (AP) and transverse (TR) vertebral neural canal dimensions together with anterior vertebral body height (BH) in thoracic (Th10–Th12) and lumbar (L1–5) vertebrae, and analysed them for association with sex, age-at-death, and burial context (individual vs mass graves). These intra-site comparisons revealed that: (1) male diameters were consistently larger than female; (2) males with stunted AP and TR diameters were less likely to survive into mature adulthood; (3) the relationship between early life stress and burial context was very weak (in females) or non-existent (in males); and (4) the TR dimension of the vertebral neural canal was more prone to growth disruption than the AP or BH diameters.