Two cases of leprosy from Žatec (Bohemia), dated to the turn of the 12th century and confirmed by DNA analysis for Mycobacterium leprae

The leprosy known today primarily from tropical areas was a relatively common disease in European Middle Ages. This article describes two skeletons bearing palaeopathological indications of leprosy from a cemetery at ?atec in North-West Bohemia (Czech Republic). The archaeological context clearly shows that these individuals were buried prior to the second decade of the 12th century, and most probably in the second half of 11th century. This rules out the possibility that these individuals might have contracted the disease in connection with the Crusades, in which a Bohemian contingent under Prince Vladislav II participated from 1141 to 1142. Molecular genetic methods were applied to detect specific DNA fragments of the causative agent of leprosy, Mycobacterium leprae. The nasal concha of one individual yielded DNA that could be directly sequenced after isolation and amplification. The vertebral body of the second individual, on the other hand, did not provide DNA of sufficient quality for direct sequencing and only weak amplification was detectable. The morphological and genetic analyses both indicate that leprosy existed prior to the Crusades in medieval Bohemia, albeit that its prevalence was probably not as great as in northern or western Europe.     

Molecular markers for the discrimination of Triticum turgidum L. subsp. dicoccum (Schrank ex Schübl.) Thell. and Triticum timopheevii (Zhuk.) Zhuk. subsp. timopheevii

The persistent uncertainty on the classification of the “new” glume wheat found in Neolithic and Bronze Age sites from Greece and other European settlements might be resolved only through analysis of its ancient DNA. Tools able to discriminate among different Triticum species on the basis of scarce, very damaged DNA, are therefore essential. While current attempts concentrate on DNA fragments sequencing and comparison, in some instances PCR-based selective amplification techniques might offer a cheaper and quicker alternative. The purpose of this research was therefore the identification of species-specific primers, able to distinguish caryopses of Triticum timopheevii subsp. timopheevii from those of Triticum turgidum subsp. dicoccum. Primers and their working conditions were defined and optimized using DNA from modern accessions. The ribosomal primers ITS1 tim and ITS2 tim, and the nuclear primer acetyl-coenzyme A tim clearly discriminated the sequences of Triticum timopheevii from other species. Finally, Neolithic charred wheat grains found in the sites of Sammardenchia (Pozzuolo del Friuli, Udine) and La Marmotta (Lago di Bracciano, Roma), belonging to the “new” wheat type or to emmer, were tested with the three selected primers. However, the results were not conclusive, because the samples analysed were apparently too degraded to yield useful DNA.     

THE TWILIGHT OF THE GODS? GENOMIC HISTORY AND THE RETURN OF RACE IN THE STUDY OF THE ANCIENT MEDITERRANEAN

This article discusses the impact of genomic history, a subdiscipline that emerged in the study of the ancient Mediterranean in the 2010s. In 2014, scientists first published a method for extracting genetic material, which they christened aDNA (ancient DNA), from ancient human remains in hot climates. After a decade of research, genomic history is now poised to transform our understanding of Mediterranean premodernity, centering migration and conflict as the key mechanisms for cultural change. Despite years of critique, aDNA researchers have failed to seriously examine the bioessentialist assumptions implicit in their work—a failure that has led many to deploy language that is strikingly evocative of pre-World War II racialism. Even worse, some genomic historians continue to make troubling overtures toward the ethnonationalist Right, which has been ascendant across Europe and North America since the 2010s. This article traces the intellectual genealogy of genomic history from World War II to the present, examines recent attempts to answer criticism from the humanities and social sciences, and suggests paths for responsible use of aDNA in historical and prehistorical scholarship.     

MtDNA haplotype identification of aurochs remains originating from the Czech Republic (Central Europe)

Abstract

This study presents the results of the analysis of mtDNA bone samples morphologically determined to be aurochs (Bos primigenius) from four various archaeological finds in the Czech Republic (Central Europe). The results from two of them — the Pleistocene sample from Praha-?eporyje and the Neolithic sample from Vedrovice — probably represent contamination by modern DNA. Sequences identified in the Eneolithic Kutná Hora-Denemark site (～5 thousand BP) confirm the presence of haplogroup P in the geographically partly isolated Czech basin. This finding (the first of its kind within the Czech Republic) is consistent with other published findings showing the domination of this aurochs haplogroup line in Europe. The combination of large individual size and ‘domestic’ mtDNA suggest, if inconclusively, that the Early Medieval fourth sample from Vy?ehrad could potentially represent an aurochs/domestic cattle hybrid.     

Repeat silica extraction: a simple technique for the removal of PCR inhibitors from DNA extracts

Polymerase chain reaction (PCR) inhibitors are often co-extracted with ancient DNA (aDNA) and when present make the analysis of aDNA difficult, if not impossible. In this study we review previous research on PCR inhibitors and techniques that address their co-extraction with DNA from sub-optimal samples. Additionally, we introduce a simple extraction technique, “repeat silica extraction,” that effectively removed PCR inhibitors from extracts of 7000–8000-year-old human skeletal remains from the Windover archaeological site in Florida and 700–2000-year-old human coprolites excavated from Fish Slough Cave in southern California. A series of tests on these same samples demonstrates that N-phenacylthiazolium bromide is largely ineffective, despite previously reported success using this compound as part of the DNA extraction process. We also describe a method for demonstrating the presence as well as successful removal of PCR inhibitors by use of a “positive aDNA control,” a test necessary to conclude that negative PCR amplification is the result of the absence of preserved DNA.     

Using ancient DNA analysis in palaeopathology: a critical analysis of published papers,with recommendations for future work

Despite an observable increase in the number of studies using ancient DNA analysis to diagnose disease in human remains, there remain issues to be addressed about the quality of the resulting publications. This paper describes the qualitative analysis of published papers that describe the detection of pathogenic DNA in human skeletal and mummified remains from archaeological sites. Its ultimate goal is to provide an overview of the main problematic issues in relationship to standards developed in molecular biology and to make recommendations for future work. Sixty‐five papers published between 1993 and 2006 were surveyed and the quality of each was assessed using 15 criteria. Interesting results emerged. Of particular note was the high number of papers that did not acknowledge the use of even basic contamination control (90%) or procedures to validate results independently (85%). This study illustrates that attention to contamination control and authentication of results is needed in future research, if confidence in aDNA analysis in palaeopathology is to be increased. Additionally, methods of analysis must be described in published papers to ensure transparency in processes utilised to generate the data. Copyright © 2008 John Wiley & Sons, Ltd.     

A pilot study into the effects of X-ray and computed tomography exposure on the amplification of DNA from bone

This research investigates the intersection of radiography and aDNA, two commonly used methods in bioarchaeology. The goal of this project was to investigate the effects of radiation on the ability to amplify DNA from bone. Bones (n = 124) from domestic pig (Sus scrofa) feet were randomly sorted into a control group and four treatment groups: (1) single exposure X-ray; (2) single exposure CT; (3) multiple exposures X-ray; and (4) multiple exposures CT. Number of PCR cycles required to amplify DNA in 100 bp, 200 bp and 400 bp segments were used as a proxy for the amount of available DNA. In the 200 bp CT sample, distal phalanges required significantly more amplification cycles than did the other bones and were removed from analysis. Results suggest that in general radiation exposure fragments DNA thereby decreasing the amount that is amplifiable. While these results are suggestive, further research is required to elucidate the degree to which radiation fragments DNA in archaeological specimens.     

Adapt or Die: Three Case Studies in Which the Failure to Adopt Advances from Other Fields has Compromised Paleopathology

Over the past several decades, the field of paleopathology has rapidly advanced, but a continuing delay in incorporating scientific advances and a lack of methodological rigor hinder its progress. Inconsistencies in the presentation of data, the persistent use of non‐standardized criteria and non‐specific skeletal lesions to diagnose diseases, and the misuse of or delay in adopting critical, relevant concepts and methods from other disciplines obfuscate the current state of evidence and unnecessarily prolong debates. Here, we present three major research questions that have been affected by these issues: the origin and antiquity of syphilis in the Old World; the pathogen responsible for the Black Death; and whether the incidence of cancer has risen in recent human history. Drawing on these examples, we conclude with recommendations that could facilitate a more rigorous, scientific approach to important questions in paleopathology. Copyright © 2015 John Wiley & Sons, Ltd.     

Molecular and osteometric sexing of cattle metacarpals: a case study from 15th century AD Beja,Portugal

In the course of a zooarchaeological survey of Holocene sites in southern Portugal, a substantial size increase of cattle bones was noted following the Christian reconquista of the 11th–13th centuries AD. A size increase in the course of time within a lineage of domestic livestock is usually considered to represent animal improvement. However several other factors including sex may influence the average size of a sample of mammal bones – cattle exhibit considerable sexual size dimorphism, with bulls being larger than cows. A histogram of the distal widths of a large (n = 44) sample of cattle metacarpals from 15th century Beja (Alentejo, Portugal), revealed a bimodal distribution. It was assumed that the large measurements belonged to males and the small to females. In order to rule out the possibility of a post-Moslem change in the sex ratio of cattle, a sub-sample of 21 cattle metacarpals from Beja was selected and we used genetic markers to identify the sex of the animals to which these metacarpals belonged. The ancient DNA sex of all specimens agreed with the previously assumed sex as determined osteometrically. We conclude that the two nearly separated peaks for the metacarpal distal width measurements do indeed indicate sex. A similar bimodal distribution was obtained from another large but earlier sample of cattle metacarpals from Moslem Alcáçova de Santarém (9th–12th century AD). Although these have not been molecularly sexed and since osteometric sexing has now been validated, we conclude that both small (female) and large (male) peaks are smaller than the 15th century ones and that there was an overall size increase or improvement of cattle in this region. Why the Christians improved cattle is unclear, but a selection for larger beeves for meat is one possibility as is the selection of more robust cattle for power. The spread of the quadrangular or chariot plough in Iberia is known to have occurred at this time. We then use the genetically sexed metacarpals to determine which measurements provide reasonable distinction between the sexes. Both the distal width (BFd; as already noted by Svensson et al., 2008; in Swedish medieval cattle) and the width of the lateral condyle (WCL) offer the best distinction. We also used them as a reference ‘collection’ to sex the medieval and post-medieval cattle metacarpals from Launceston Castle in England. This re-visit of the Launceston data corroborates other evidence indicating increased specialisation (milk and veal) in post-medieval cattle husbandry in England.     

Tuberculosis on the north coast of Peru: skeletal and molecular paleopathology of late pre-Hispanic and postcontact mycobacterial disease

This paper examines skeletal and ancient DNA evidence in the study of suspected tuberculosis infection in the late pre-Hispanic and Colonial-era Lambayeque Valley Complex, north coast Peru (A.D. 900–1750). We integrate information on macroscopic lesion characteristics and distribution, radiographic and CT scan imagery, and analysis of Mycobacterium tuberculosis complex rpoB and IS6110 ancient DNA (aDNA) sequences. Destructive lesions were observed in the vertebral bodies of three precontact indigenous adult males, one colonial adolescent female, and in the cranium of a Colonial-period subadult. Assessment of lesion morphology and distribution led us to consider multiple diseases, but tuberculosis represents the most likely diagnostic option in all individuals. DNA was poorly preserved in all samples, but an IS6110 sequence was amplified in one precontact individual consistent with macroscopic diagnosis. These findings expand the geographic and temporal extent of tuberculosis to the late pre-Hispanic and Colonial north coast of Peru to highlight potential synergisms between diet, settlement patterns, and the evolution of Andean tuberculosis before and after European conquest. Moreover, this study helps focus several key questions in Andean tuberculosis research, including possible reassessment of the presence of the IS6110 sequence in the pre-Columbian Americas. Methodological considerations include differential diagnosis – especially with incomplete skeletons – and limitations of aDNA studies underscoring an approach integrating macroscopic, radiographic, and molecular lines of evidence in the paleopathological investigation of one of humankind’s most devastating and destabilizing diseases.