False positives complicate ancient pathogen identifications using high-throughput shotgun sequencing

Background: Identification of historic pathogens is challenging since false positives and negatives are a serious risk. Environmental non-pathogenic contaminants are ubiquitous. Furthermore, public genetic databases contain limited information regarding these species. High-throughput sequencing may help reliably detect and identify historic pathogens. Results: We shotgun-sequenced 8 16th-century Mixtec individuals from the site of Teposcolula Yucundaa (Oaxaca, Mexico) who are reported to have died from the huey cocoliztli (‘Great Pestilence’ in Nahautl), an unknown disease that decimated native Mexican populations during the Spanish colonial period, in order to identify the pathogen. Comparison of these sequences with those deriving from the surrounding soil and from 4 precontact individuals from the site found a wide variety of contaminant organisms that confounded analyses. Without the comparative sequence data from the precontact individuals and soil, false positives for Yersinia pestis and rickettsiosis could have been reported. Conclusions: False positives and negatives remain problematic in ancient DNA analyses despite the application of high-throughput sequencing. Our results suggest that several studies claiming the discovery of ancient pathogens may need further verification. Additionally, true single molecule sequencing’s short read lengths, inability to sequence through DNA lesions, and limited ancient-DNA-specific technical development hinder its application to palaeopathology

Increasing variability of body mass and health correlates in Swiss conscripts, a possible role of relaxed natural selection?

Background and objectives The body mass index (BMI) is an established anthropometric index for the development of obesity related conditions. However, little is known about the distribution of BMI within a population, especially about this distribution’s temporal change. Here, we analysed changes in the distribution of height, weight and BMI over the past 140 years based on data of Swiss conscripts and tested for correlations between anthropometric data and standard blood parameters. Methods Height and weight were measured in 59,504 young Swiss males aged 18-19 years during conscription in 1875-79, 1932-36, 1994 and 2010-12. For 65% of conscripts in 2010-12 results of standard blood analysis were available. We calculated descriptive statistics of the distribution of height, weight, and BMI over the four time periods and tested for associations between BMI and metabolic parameters. Results Average and median body height, body weight and BMI increased over time. Height did no longer increase between 1994 and 2010-12, while weight and BMI still increased over these two decades. Variability ranges of weight and BMI increased over time, while variation of body height remained constant. Elevated levels of metabolic and inflammatory blood parameters were found at both ends of BMI distribution. Conclusions and Implications Both overweight and underweight subgroups showed similar changes in inflammation parameters, pointing towards related metabolic deficiencies in both conditions. In addition to environmental influences, our results indicate a potential role of relaxed natural selection on genes affecting metabolism and body composition

Metagenomic analysis of Ancient Egyptian canopic jars

Ancient Egyptian remains have been of interest for anthropological research for decades. Despite many investigations, the ritual vessels for the internal organs removed during body preparation—liver, lungs, stomach, and intestines, of Egyptian mummies are rarely used for palaeopathological or medical investigations. These artifacts, commonly referred to as canopic jars, are the perfect combination of cultural and biological material and present an untapped resource for both Egyptological and medical fields. Nevertheless, technical challenges associated with this archeological material have prevented the application of current ancient DNA techniques for both the characterization of human and pathogenic DNA. We present shotgun-sequenced metagenomic profiles and ancient DNA degradation patterns from multiple canopic jars sampled from several European museum collections and enumerate current limitations and possible solutions for the future analysis of similar material. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars and the first associated metagenomic description of bacterial taxa in these funerary artifacts. Objectives In this study, our objectives were to characterize the metagenomic profile of the Ancient Egyptian funerary vessels known as canopic jars to retrieve endogenous ancient human DNA, reconstruct ancient microbial communities, and identify possible pathogens that could shed light on disease states of individuals from the past. Methods We applied ancient DNA techniques on 140 canopic jars to extract DNA and generate whole-genome sequencing libraries for the analysis of both human and bacterial DNA. The samples were obtained from museum collections in Berlin (DE), Burgdorf (DE), Leiden (NE), Manchester (UK), Munich (DE), St. Gallen (CH), Turin (IT), and Zagreb (HR). Results Here we describe the first isolated DNA from the Egyptian artifacts that hold human viscera. No previous work was ever conducted on such material, which led to the first characterization of human DNA from Ancient Egyptian canopic jars and the profiling of the complex bacterial composition of this highly degraded, challenging, organic material. However, the DNA recovered was not of enough quality to confidently characterize bacterial taxa associated with infectious diseases, nor exclusive bacterial members of the human microbiome. Discussion In summary, we present the first genomic survey of the visceral content of Ancient Egyptian funerary artifacts and demonstrate the limitations of current molecular methods to analyze canopic jars, such as the incomplete history of the objects or the presence of uncharacterized compounds that can hamper the recovery of DNA. Our work highlights the main challenges and caveats when working with such complicated archeological material – and offers sampling recommendations for similarly complex future studies, such as incrementing the amount of starting material and sampling from the less exposed parts of the jar content. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars, and our results open new avenues in the study of neglected archeological artifacts

The Mummy Explorer—a self-regulated open-access online teaching tool

Background and objectives: Virtual teaching tools have gained increasing importance in recent years. In particular, the COVID-19 pandemic has reinforced the need for media-based and self-regulated tools. What is missing are tools that allow us to interlink highly interdisciplinary fields such as evolutionary medicine and, at the same time, allow us to adapt content to different lectures. Methodology: We designed an interactive online teaching tool, namely, the Mummy Explorer, using open-access software (Google Web Designer), and we provided a freely downloadable template. We tested the tool on students and lecturers of evolutionary medicine using questionnaires and improved the tool according to their feedback. Results: The tool has a modular design and provides an overview of a virtual mummy excavation, including the subfields of palaeopathology, paleoradiology, cultural and ethnographic context, provenance studies, paleogenetics, and physiological analyses. The template allows lecturers to generate their own versions of the tool for any topic of interest by simply changing the text and pictures. Tests undertaken with students of evolutionary medicine showed that the tool was helpful during their studies. Lecturers commented that they appreciated having a similar tool in other fields. Conclusions and implications: Mummy Explorer fills a gap in the virtual teaching landscape of highly interdisciplinary fields such as evolutionary medicine. It will be offered for free download and can be adapted to any educational topic. Translations into German and possibly other languages are in progress

Gout in Duke Federico of Montefeltro (1422-1482): a new pearl of the Italian Renaissance

The article examines the truthfulness of historical accounts claiming that Renaissance Duke Federico of Montefeltro (1422-1482) suffered from gout. By direct paleopathological assessment of the skeletal remains and by the philological investigation of historical and documental sources, primarily a 1461 handwritten letter by the Duke himself to his personal physician, a description of the symptoms and Renaissance therapy is offered and a final diagnosis of gout is formulated. The Duke's handwritten letter offers a rare testimony of ancient clinical self-diagnostics and Renaissance living-experience of gout. Moreover, the article also shows how an alliance between historical, documental and paleopathological methods can greatly increase the precision of retrospective diagnoses, thus helping to shed clearer light onto the antiquity and evolution of diseases

A tall order: Small area mapping and modelling of adult height among Swiss male conscripts

Adult height reflects an individual's socio-economic background and offers insights into the well-being of populations. Height is linked to various health outcomes such as morbidity and mortality and has consequences on the societal level. The aim of this study was to describe small-area variation of height and associated factors among young men in Switzerland. Data from 175,916 conscripts (aged between 18.50 and 20.50 years) was collected between 2005 and 2011, which represented approximately 90% of the corresponding birth cohorts. These were analysed using Gaussian hierarchical models in a Bayesian framework to investigate the spatial pattern of mean height across postcodes. The models varied both in random effects and degree of adjustment (professional status, area-based socioeconomic position, and language region). We found a strong spatial structure for mean height across postcodes. The range of height differences between mean postcode level estimates was 3.40cm according to the best fitting model, with the shorter conscripts coming from the Italian and French speaking parts of Switzerland. There were positive socioeconomic gradients in height at both individual and area-based levels. Spatial patterns for height persisted after adjustment for individual factors, but not when language region was included. Socio-economic position and cultural/natural boundaries such as language borders and mountain passes are shaping patterns of height for Swiss conscripts. Small area mapping of height contributes to the understanding of its cofactors