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The plague of 1630–1632 was one of the deadliest plague epidemics to ever hit Northern Italy, and for many of the affected regions, it was also the last. While accounts on plague during the early 1630s in Florence and Milan are frequent, much less is known about the city of Imola. We analyzed the full skeletal assemblage of four mass graves (n = 133 individuals) at the Lazaretto dell’Osservanza, which date back to the outbreak of 1630–1632 in Imola and evaluated our results by integrating new archival sources. The skeletons showed little evidence of physical trauma and were covered by multiple layers of lime, which is characteristic for epidemic mass mortality sites. We screened 15 teeth for Yersinia pestis aDNA and were able to confirm the presence of plague in Imola via metagenomic analysis. Additionally, we studied a contemporaneous register, in which a friar recorded patient outcomes at the lazaretto during the last year of the epidemic. Our multidisciplinary approach combining historical, osteological and genomic data provided a unique opportunity to reconstruct an in-depth picture of the last plague of Imola through the city's main lazaretto.

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally1, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups2, 3 has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa4, although a much younger origin has also been proposed5. The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1’s evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 × 10-7 Introduction Results - Retrieved genomes are likely from typical infections - Demographic history of HSV-1 in a global context Discussion Material and Methods - Ethics statement - Sampling - Generation of aDNA libraries - Sequencing - aDNA authentication - Metagenomic screening - Targeted capture of HSV-1 - Alignment of viral data to the reference sequence - Genotyping - HSV-1 linkage disequilibrium and population genetic analysis - Compilation of comparative HSV data - Preparation of genome sequences - HSV-1 phylogenetic analysis and recombination filtering - Phylogenetic dating - Alignment of human data to the reference sequence and quality control - Genetic sex estimation, mtDNA, and Y haplotyping - Human variant calling and imputation of genotypes

Ancient DNA from Yersinia pestis has been identified in skeletons at four urban burial grounds in Cambridge, England, and at a nearby rural cemetery. Dating to between ad 1349 and 1561, these represent individuals who died of plague during the second pandemic. Most come from normative individual burials, rather than mass graves. This pattern represents a major advance in archaeological knowledge, shifting focus away from a few exceptional discoveries of mass burials to what was normal practice in most medieval contexts. Detailed consideration of context allows the authors to identify a range of burial responses to the second pandemic within a single town and its hinterland. This permits the creation of a richer and more varied narrative than has previously been possible.

Significance The spread and evolution of plague have been under debate in the past few years. However, very little is known of the dynamics of the plague pathogen, Yersinia pestis, during the last phase of the Second Plague Pandemic in Europe (18th and 19th century). We present nine ancient Y. pestis genomes from the Second Plague Pandemic. CHE1 is the first Second Plague Pandemic genome from the Caucasus region, an area that houses plague wildlife reservoirs to this day, making it a key strain to help elucidate the origin of Medieval and Early Modern plague. Our study documents the importance of a noneurocentric approach to historical plague dynamics and proposes an origin of plague introductions outside of Europe., Plague continued to afflict Europe for more than five centuries after the Black Death. Yet, by the 17th century, the dynamics of plague had changed, leading to its slow decline in Western Europe over the subsequent 200 y, a period for which only one genome was previously available. Using a multidisciplinary approach, combining genomic and historical data, we assembled Y. pestis genomes from nine individuals covering four Eurasian sites and placed them into an historical context within the established phylogeny. CHE1 (Chechnya, Russia, 18th century) is now the latest Second Plague Pandemic genome and the first non-European sample in the post-Black Death lineage. Its placement in the phylogeny and our synthesis point toward the existence of an extra-European reservoir feeding plague into Western Europe in multiple waves. By considering socioeconomic, ecological, and climatic factors we highlight the importance of a noneurocentric approach for the discussion on Second Plague Pandemic dynamics in Europe.

Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals’ oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th–6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons’ oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.

The Early Iron Age nomadic Scythians have been described as a confederation of tribes of different origins, based on ancient DNA evidence [1-3]. It is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome sequences of 31 ancient Western and Eastern Steppe individuals, including Scythians as well as samples pre- and postdating them, allowing us to set the Scythians in a temporal context (in the Western, i.e., Ponto-Caspian Steppe). We detect an increase of eastern (Altaian) affinity along with a decrease in eastern hunter-gatherer (EHG) ancestry in the Early Iron Age Ponto-Caspian gene pool at the start of the Scythian dominance. On the other hand, samples of the Chernyakhiv culture postdating the Scythians in Ukraine have a significantly higher proportion of Near Eastern ancestry than other samples of this study. Our results agree with the Gothic source of the Chernyakhiv culture and support the hypothesis that the Scythian dominance did involve a demic component.

Significance Louse-borne relapsing fever was one of the major diseases affecting Western human populations, with its last major pandemic killing millions after World War I. Despite the major role fevers have played in epidemic events throughout history, molecular evidence for the presence of their etiological agent has been extremely scarce in historical samples worldwide. By comparing our medieval Borrelia recurrentis genome with modern representatives of the species, we offer an historical snapshot of genomic changes in an immune-evasion system and of reductive evolution in a specialized vector-borne human pathogen. This shotgun sequencing project highlights the potential for ancient DNA research to uncover pathogens which are undetectable to osteological analysis but are known to have played major roles in European health historically., Louse-borne relapsing fever (LBRF) is known to have killed millions of people over the course of European history and remains a major cause of mortality in parts of the world. Its pathogen, Borrelia recurrentis, shares a common vector with global killers such as typhus and plague and is known for its involvement in devastating historical epidemics such as the Irish potato famine. Here, we describe a European and historical genome of B. recurrentis, recovered from a 15th century skeleton from Oslo. Our distinct European lineage has a discrete genomic makeup, displaying an ancestral oppA-1 gene and gene loss in antigenic variation sites. Our results illustrate the potential of ancient DNA research to elucidate dynamics of reductive evolution in a specialized human pathogen and to uncover aspects of human health usually invisible to the archaeological record.

Significance While our knowledge of modern plague reservoirs and their hosts is extensive, we have little to no knowledge about the origin of the Medieval plague pandemics or the routes of transmission involved in their spread. Prior genomic data provide a patchy low-resolution picture of the transmission dynamics involved during the Second Plague Pandemic, with only five distinct genomes. We have reevaluated all Medieval strains under the light of archaeological and historical evidence to carefully discuss the involvement of different transmission routes during the Second Plague Pandemic. Our interpretation showcases the importance of trade routes and human movements and further supports the identification of Yersinia pestis as the pathogenic agent of the so-called pestis secunda (1357–1366)., Over the last few years, genomic studies on Yersinia pestis, the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the second half of the 14th century and reconstruct the evolutionary history of Y. pestis by reanalyzing previously published genomes and by building a comprehensive phylogeny focused on strains attributed to the Second Plague Pandemic (14th to 18th century). Corroborated by historical and ecological evidence, the presented phylogeny, which includes our Y. pestis genomes, could support the hypothesis of an entry of plague into Western European ports through distinct waves of introduction during the Medieval Period, possibly by means of fur trade routes, as well as the recirculation of plague within the human population via trade routes and human movement.