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.
Highlights d Genome-wide analysis of 110 ancient individuals from the Near East d Gene pools of Anatolia and Caucasus were biologically connected 6500 BCE d Gene flow from neighboring populations in Northern Levant during 3 rd millennium BCE d One individual of likely Central Asian origin in 2 nd millennium BCE Northern Levant
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.
Highlights d An Upper Paleolithic Siberian shows a deep link with the First Peoples of the Americas d A 10,000-year continuum of Ancient North Eurasian ancestry in the Lake Baikal region d The Neolithic to Bronze Age population formation occurred through prolonged local admixture d Long-range human and Y. pestis mobility across Eurasia during the Early Bronze Age
It has been hypothesized that the Neolithic transition towards an
agricultural and pastoralist economy facilitated the emergence of human adapted
pathogens. Here, we recovered eight
Salmonella enterica
subsp.
enterica
genomes from human skeletons of transitional
foragers, pastoralists, and agro-pastoralists in western Eurasia that were up to
6,500 years old. Despite the high genetic diversity of
S.
enterica
all ancient bacterial genomes clustered in a single
previously uncharacterized branch that contains
S. enterica
adapted to multiple mammalian species. All ancient bacterial genomes from
prehistoric (agro-)pastoralists fall within a part of this branch that also
includes the human-specific
S. enterica
Paratyphi C,
illustrating the evolution of a human pathogen over a period of five thousand
years. Bacterial genomic comparisons suggest that the earlier ancient strains
were not host specific, differed in pathogenic potential, and experienced
convergent pseudogenization that accompanied their downstream host adaptation.
These observations support the concept that the emergence of human adapted
S. enterica
is linked to human cultural
transformations.
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