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Open AccessAncient Plasmodium genomes shed light on the history of human malaria
Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach...
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Open AccessOrigin and dispersal history of Hepatitis B virus in Eastern Eurasia
Hepatitis B virus is a globally distributed pathogen and the history of HBV infection in humans predates 10000 years. However, long-term evolutionary history of HBV in Eastern Eurasia remains elusive. We prese...
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Open AccessGeographically dispersed zoonotic tuberculosis in pre-contact South American human populations
Previous ancient DNA research has shown that Mycobacterium pinnipedii, which today causes tuberculosis (TB) primarily in pinnipeds, infected human populations living in the coastal areas of Peru prior to European...
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Open AccessUsing Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe
Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal...
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Open Access2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals
Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiom...
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Open AccessA seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex
Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MT...
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Open AccessA treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15th century Europe
Developments in techniques for identification of pathogen DNA in archaeological samples can expand our resolution of disease detection. Our application of a non-targeted molecular screening tool for the parall...
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Emergence of human-adapted Salmonella enterica is linked to the Neolithization process
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. ent...
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Open AccessHOPS: automated detection and authentication of pathogen DNA in archaeological remains
High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from arc...
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Open AccessPhylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes
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 spannin...
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Ancient pathogen genomics as an emerging tool for infectious disease research
Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of p...
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Open AccessAnalysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague
The origin of Yersinia pestis and the early stages of its evolution are fundamental subjects of investigation given its high virulence and mortality that resulted from past pandemics. Although the earliest eviden...
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Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico
Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic ag...
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Open AccessCentral European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes
The population dynamics of the Pleistocene woolly mammoth (Mammuthus primigenius) has been the subject of intensive palaeogenetic research. Although a large number of mitochondrial genomes across Eurasia have bee...
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Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster
The abrupt onslaught of the syphilis pandemic that started in the late fifteenth century established this devastating infectious disease as one of the most feared in human history1. Surprisingly, despite the avai...
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Open AccessEffect of X-ray irradiation on ancient DNA in sub-fossil bones – Guidelines for safe X-ray imaging
Sub-fossilised remains may still contain highly degraded ancient DNA (aDNA) useful for palaeogenetic investigations. Whether X-ray computed [micro-] tomography ([μ]CT) imaging of these fossils may further dama...
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Open AccessEAGER: efficient ancient genome reconstruction
The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.
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Open AccessMitochondrial Genomes of Giant Deers Suggest their Late Survival in Central Europe
The giant deer Megaloceros giganteus is among the most fascinating Late Pleistocene Eurasian megafauna that became extinct at the end of the last ice age. Important questions persist regarding its phylogenetic re...
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Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis
Three 1,000-year-old mycobacterial genomes from Peruvian human skeletons reveal that a member of the Mycobacterium tuberculosis complex derived from seals caused human disease before contact in the Americas.
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Open AccessAltering gene expression by aminocoumarins: the role of DNA supercoiling in Staphylococcus aureus
It has been shown previously that aminocoumarin antibiotics such as novobiocin lead to immediate downregulation of recA expression and thereby inhibit the SOS response, mutation frequency and recombination capaci...
