No abstract

The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. 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 a Y. pestis lineage 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 of Y. pestis during both events.

The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium’s spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.

Comparison of funerary treatment and skeletal biology can be very informative about the interplay of social status and meanings and actual life conditions in ancient communities, but such comparison is rarely done, due in part to the disciplinary separation of bioanthropology and social archaeology in many archaeological traditions. In this paper, we analyze relations between skeletal pathologies and grave goods in a sample of 94 individuals from Pontecagnano (Salerno, Italy, seventh-third centuries BC). The results show that the relationship between health, activity, and social status as expressed in grave goods was complex. Some biological indicators considered typical of "stress" or biological status (enamel hypoplasia, cribra orbitalia, adult stature) bore no relation to social status. Other indicators, particularly those of activity and stress in adult life (trauma, Schmorl's nodes, periostitis), covaried with grave assemblage and help to outline a possible division of labor. As this analysis shows, when skeletal and archaeological data are used in conjunction, the result is a deeper picture of the social and economic life of the community than can be obtained from either source.

Funerary taphonomy has come of age as an important field in osteoarchaeology. Its goal is to reconstruct funerary practices by using taphonomic evidence, including both evidence recorded during excavation (particularly the context and state of articulation of human remains) and evidence observable in subsequent laboratory analysis (such as element representation and traces of burning, animal modification, cut-marks, and fragmentation). This articleintended as a systematic introduction to the fieldgives an overview of funerary taphonomy. It first discusses the goals and theoretical questions, and then reviews the wide range of methods available to archaeologists using human remains to investigate funerary behaviour. It finishes with a review of how taphonomists have approached particular issues, such as single burials, commingled multiple depositions, cannibalism, and the cultural reuse of human skeletal parts.