The posterior portion of the ilium as a sex indicator:A validation study

Establishing a biological profile of skeletal remains is a key task of forensic anthropologists. Sex estimation is essential in forensic examination, as other elements of the biological profile, such as age at death or stature, are sex dependent. Visual assessment is considered low-cost and quick, therefore it is a commonly applied method of sex estimation. The most reliable results can be obtained with the analysis of the anterior part of the pelvis, however, these skeletal elements are fragile and prone to destruction. In contrary, the more robust posterior portion of the pelvis is often recovered. Several features of the posterior pelvis have been explored in the context of sexual dimorphism. The aim of the present study was to test three previously published methods of sex assessment based on the analysis of the inferior shape of the auricular surface (Novotný, 1975), the greater sciatic notch shape (Walker, 2005 (revised)) and overall morphology, apex morphology and inflection of the auricular surface (Luna et al., 2017). The sample consisted of 194 individuals of Greek origin from a documented modern collection. Four features of the auricular surface and shape of the greater sciatic notch were examined. Logistic regression analysis was applied to produce a sex discriminatory formula. The method proposed by Luna et al. (2017) failed to produce satisfactory results with overall accuracies of 36%, 50% and 53% for overall morphology, apex morphology and inflection respectively. Slightly better results (64%) were obtained with the inferior shape morphology (Novotný, 1975). However, the highest accuracy rate of 81% was noted for the greater sciatic notch shape (Walker, 2005 (revised)). The formula produced in this study allowed correct classification of 83.2% of the sample. This study illustrates that in spite of the presence of sexual dimorphism in the posterior portion of ilium, features of the auricular surface proposed as sex indicators by Novotný (1975) and Luna et al. (2017) should not be used for sex estimation purposes in the Greek population. The formula produced in this study and the greater sciatic notch shape should only be used as additional methods in cases where neither the cranium nor the anterior portion of the pelvis is present

Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic

Ancient genomic studies have identified Yersinia pestis (Y. pestis) as the causative agent of the second plague pandemic (fourteenth-eighteenth century) that started with the Black Death (1,347-1,353). Most of the Y. pestis strains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence of Y. pestis sequences in four remains, confirming that the buried individuals were victims of plague. In two samples, Y. pestis DNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the Riga strains fell within the diversity of the already known post-Black Death genomes. Interestingly, the two Latvian isolates did not cluster together. Moreover, we detected a drop in coverage of the pPCP1 plasmid region containing the pla gene. Further analysis indicated the presence of two pPCP1 plasmids, one with and one without the pla gene region, and only one bacterial chromosome, indicating that the same bacterium carried two distinct pPCP1 plasmids. In addition, we found the same pattern in the majority of previously published post-Black Death strains, but not in the Black Death strains. The pla gene is an important virulence factor for the infection of and transmission in humans. Thus, the spread of pla-depleted strains may, among other causes, have contributed to the disappearance of the second plague pandemic in eighteenth century Europe

Ancient DNA investigation into infectious diseases of medieval Europe

Infectious diseases have been a burden to human populations around the globe, posing an immense selective pressure on our genomes. Moreover, the constant evolution of pathogens poses a major threat to human health. In my dissertation, I applied ancient genomics to investigate the pathogen diversity and infectious disease burden in medieval Europe as well as to identify Human Leukocyte Antigens (HLA) alleles involved in predisposition to infections. In chapter 1, I identified the HLA-DRB1*03 as a risk factor for Salmonella infection in medieval Europeans. In the case-control association study between HLA alleles and medieval leprosy (chapter 2), I reported five alleles linked to leprosy predisposition in Europeans. The pathogen screening of the early medieval settlement in chapter 3 allowed me to estimate the infection prevalence at the time (~ 31.4%). Seven genomes belonging to four pathogen species (Mycobacterium leprae, variola virus, parvovirus B19 and hepatitis B virus) were reconstructed and analyzed. In chapter 4, the genomic analysis of medieval Yersinia pestis strains revealed the depletion of the virulence-associated pla gene exclusively in isolates dating to the end of the Medieval pandemic. In the following chapter 5, I demonstrated that only a subset of modern strains carried a phage encoding the zonula occludens toxin– a known virulence factor. The phage-positive strains were associated with a wide geographic spread and a large proportion of human infections. In chapter 6, I provided evidence that plague victims were not exclusively buried in mass graves in medieval Denmark, but also at parish cemeteries. The findings presented in my dissertation contribute to a better understanding of the host-pathogen coevolution and the genetic implications of past epidemics on our health today

Ancient DNA Study in Medieval Europeans Shows an Association Between HLA-DRB1*03 and Paratyphoid Fever

Outbreaks of infectious diseases repeatedly affected medieval Europe, leaving behind a large number of dead often inhumed in mass graves. Human remains interred in two burial pits from 14th century CE Germany exhibited molecular evidence of Salmonella enterica Paratyphi C (S. Paratyphi C) infection. The pathogen is responsible for paratyphoid fever, which was likely the cause of death for the buried individuals. This finding presented the unique opportunity to conduct a paratyphoid fever association study in a European population. We focused on HLA-DRB1*03:01 that is a known risk allele for enteric fever in present-day South Asians. We generated HLA profiles for 29 medieval S. Paratyphi C cases and 24 contemporaneous controls and compared these to a modern German population. The frequency of the risk allele was higher in the medieval cases (29.6%) compared to the contemporaneous controls (13%; p = 0.189), albeit not significantly so, possibly because of small sample sizes. Indeed, in comparison with the modern controls (n = 39,689; 10.2%; p = 0.005) the frequency difference became statistically significant. This comparison also suggested a slight decrease in the allele’s prevalence between the medieval and modern controls. Up to now, this is the first study on the genetic predisposition to Salmonella infection in Europeans and the only association analysis on paratyphoid fever C. Functional investigation using computational binding prediction between HLA variants and S. Paratyphi and S. Typhi peptides supported a reduced recognition capacity of bacterial proteins by DRB1*03:01 relative to other common DRB1 variants. This pattern could potentially explain the disease association. Our results suggest a slightly reduced predisposition to paratyphoid fever in modern Europeans. The causative allele, however, is still common today, which can be explained by a trade-off, as DRB1*03:01 is protective against infectious respiratory diseases such as severe respiratory syndrome (SARS). It is thus possible that the allele also provided resistance to corona-like viruses in the past

Pathogen genomics study of an early medieval community in Germany reveals extensive co-infections.

Funder: Universitätsklinikum Schleswig-Holstein - Campus Kiel (6509)BACKGROUND: The pathogen landscape in the Early European Middle Ages remains largely unexplored. Here, we perform a systematic pathogen screening of the rural community Lauchheim "Mittelhofen," in present-day Germany, dated to the Merovingian period, between fifth and eighth century CE. Skeletal remains of individuals were subjected to an ancient DNA metagenomic analysis. Genomes of the detected pathogens were reconstructed and analyzed phylogenetically. RESULTS: Over 30% of the individuals exhibit molecular signs of infection with hepatitis B virus (HBV), parvovirus B19, variola virus (VARV), and Mycobacterium leprae. Seven double and one triple infection were detected. We reconstructed four HBV genomes and one genome each of B19, VARV, and M. leprae. All HBV genomes are of genotype D4 which is rare in Europe today. The VARV strain exhibits a unique pattern of gene loss indicating that viruses with different gene compositions were circulating in the Early Middle Ages. The M. leprae strain clustered in branch 3 together with the oldest to-date genome from the UK. CONCLUSIONS: The high burden of infectious disease, together with osteological markers of physiological stress, reflect a poor health status of the community. This could have been an indirect result of the climate decline in Europe at the time, caused by the Late Antique Little Ice Age (LALIA). Our findings suggest that LALIA may have created an ecological context in which persistent outbreaks set the stage for major epidemics of severe diseases such as leprosy and smallpox hundreds of years later