The second plague pandemic, caused byYersinia pestis, devastated Europe and the nearby regions between the 14^thand 18^thcenturies AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancientY. pestisgenomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of aY. pestislineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541–750 AD), suggesting a comparable evolutionary trajectory ofY. pestisduring both events.

Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16^th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom—a skeleton from the Great Chesterford cemetery with a calibrated age of 415–545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide. Many controversies surround leprosy, which is one of the oldest recorded diseases of humankind. The origin and past spread of its main causative agent, Mycobacterium leprae, remain unknown although many attempts have been made to reconstruct its past from historical and archeological sources. Analysis of ancient M. leprae genomes reconstructed from archaeological remains can contribute greatly to reconstructing the origin and evolution of this pathogen. With a new set of ancient M. leprae genomes from Europe, we traced back a so far unrecognized past diversity, which places Europe as a key region for the early spread and worldwide dissemination of leprosy. Our results hint to the potential dynamic changes in the prevalence of different M. leprae strains in Europe during Antiquity, and highlight the need to study ancient pathogen genomes in order to better understand our past.

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 fourM. lepraelineages in some parts of Europe since the Early Medieval period.Results: Here, we reconstructed 19 ancientM. lepraegenomes to further investigateM. leprae’sgenetic 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 ancientM. lepraegenomes, our results improve our knowledge of the past phylogeography ofM. lepraeand reveal a particularly highM. lepraediversity 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 ofM. 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 ancientM. lepraegenomes worldwide improves our understanding of leprosy’s global history and can contribute to current models ofM. leprae’s worldwide dissemination, including interspecies transmissions.

We have examined a 5th to 6th century inhumation from Great Chesterford, Essex, UK. The incomplete remains are those of a young male, aged around 21–35 years at death. The remains show osteological evidence of lepromatous leprosy (LL) and this was confirmed by lipid biomarker analysis and ancient DNA (aDNA) analysis, which provided evidence for both multi-copy and single copy loci from the Mycobacterium leprae genome. Genotyping showed the strain belonged to the 3I lineage, but the Great Chesterford isolate appeared to be ancestral to 3I strains found in later medieval cases in southern Britain and also continental Europe. While a number of contemporaneous cases exist, at present, this case of leprosy is the earliest radiocarbon dated case in Britain confirmed by both aDNA and lipid biomarkers. Importantly, Strontium and Oxygen isotope analysis suggest that the individual is likely to have originated from outside Britain. This potentially sheds light on the origins of the strain in Britain and its subsequent spread to other parts of the world, including the Americas where the 3I lineage of M. leprae is still found in some southern states of America.

Objectives: In tests on known individuals macroscopic sex estimation has between 70% and 98% accuracy. However, materials used to create and test these methods are overwhelming modern. As sexual dimorphism is dependent on multiple factors, it is unclear whether macroscopic methods have similar success on earlier materials, which differ in lifestyle and nutrition. This research aims to assess the accuracy of commonly used traits by comparing macroscopic sex estimates to genetic sex in medieval English material.Materials and Methods: Sixty‐six individuals from the 13th to 16th century Hospital of St John the Evangelist, Cambridge, were assessed. Genetic sex was determined using a shotgun approach. Eighteen skeletal traits were examined, and macroscopic sex estimates were derived from the os coxae, skull, and os coxae and skull combined. Each trait was tested for accuracy to explore sex estimates errors.Results: The combined estimate (97.7%) outperformed the os coxae only estimate (95.7%), which outperformed the skull only estimate (90.4%). Accuracy rates for individual traits varied: Phenice traits were most accurate, whereas supraorbital margins, frontal bossing, and gonial flaring were least accurate. The preauricular sulcus and arc compose showed a bias in accuracy between sexes.Discussion: Macroscopic sex estimates are accurate when applied to medieval material from Cambridge. However, low trait accuracy rates may relate to differences in dimorphism between the method derivative sample and the St John's collection. Given the sex bias, the preauricular sulcus, frontal bossing, and arc compose should be reconsidered as appropriate traits for sex estimation for this group.

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating from the 3rd to 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. Considering a dataset of modern and ancient genomes, we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 to 5.65) ka. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60 to 6.12) ka, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations.