Yersinia pestis DNA from Skeletal Remains from the 6(th) Century AD Reveals Insights into Justinianic Plague.

Yersinia pestis, the etiologic agent of the disease plague, has been implicated in three historical pandemics. These include the third pandemic of the 19(th) and 20(th) centuries, during which plague was spread around the world, and the second pandemic of the 14(th)-17(th) centuries, which included the infamous epidemic known as the Black Death. Previous studies have confirmed that Y. pestis caused these two more recent pandemics. However, a highly spirited debate still continues as to whether Y. pestis caused the so-called Justinianic Plague of the 6(th)-8(th) centuries AD. By analyzing ancient DNA in two independent ancient DNA laboratories, we confirmed unambiguously the presence of Y. pestis DNA in human skeletal remains from an Early Medieval cemetery. In addition, we narrowed the phylogenetic position of the responsible strain down to major branch 0 on the Y. pestis phylogeny, specifically between nodes N03 and N05. Our findings confirm that Y. pestis was responsible for the Justinianic Plague, which should end the controversy regarding the etiology of this pandemic. The first genotype of a Y. pestis strain that caused the Late Antique plague provides important information about the history of the plague bacillus and suggests that the first pandemic also originated in Asia, similar to the other two plague pandemics

Ancient DNA is preserved in fish fossils from tropical lake sediments

Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia

Yersinia pestis: der Erreger des Schwarzen Todes

Within the last 1.500 years, millions of people have died during three historical plague pandemics. Nowadays, modern medicine and preventative measures can contain the outbreaks, but plague becomes a risk when bacteria acquire new resistance genes. The deep knowledge of all modern and historical forms of Yersinia pestisis of great importance to understand its evolution, its virulence, and the mechanisms and routes of dissemination. This can help in efficiently avoiding dangerous epidemics in the future

The pla gene, encoding plasminogen activator, is not specific to Yersinia pestis

Here we present evidence to show that the pla gene, previously thought to be specific to Yersinia pestis, occurs in some strains of Citrobacter koseri and Escherichia coli. This means that detection of this gene on its own can no longer be taken as evidence of detection of Y. pestis

Evolutionary consequences of the past pandemics

In historical times epidemics and pandemics killed large proportions of the European population, with likely consequences for the human genome as a result of positive selection acting on protective alleles. Pathophysiological evidence has suggested, for example, that cystic fibrosis mutations may confer resistance to cholera or other chloride-secreting diarrhoeas, whereas a high incidence of the CCR5-Delta32 mutation, which nowadays plays a substantial role in immunity against HIV-I infection, has been proposed to have provided some immunity against plague (...............

Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period

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

Individuals from the Early Medieval Cemetery Aschheim-Bajuwarenring (Germany) that were analyzed in this study and corresponding results of screening for a portion of the <i>Y. pestis</i> specific <i>plasminogen activator gene</i> (<i>pla</i>).

1<p>estimated age by archaeological evidence <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-GutsmiedlSchmann1" target="_blank">[20]</a> for the multiple burial,</p>2<p>estimated age by radiocarbon dating determined for the particular individual (cal 2 sigma),</p>3<p>neg = no amplicon, pos = amplification results, - = not tested.</p

Results of molecular assays carried out on samples from individual A120 in two independent aDNA laboratories.

<p>Abbreviations: anc: ancestral, der: derived, pos: positive, <i>pla</i>: plasminogen activator gene, -: not tested, neg: no amplicon.</p