75 research outputs found

    Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750)

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    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. © 2019 National Academy of Sciences. All rights reserved

    Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

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    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 × 10-7Introduction 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 genotype

    The synthesis, structures and reactions of zinc and cobalt metal-organic frameworks incorporating an alkyne-based dicarboxylate linker

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    The reaction of zinc(II) nitrate and 4,4′-ethynylenedibenzoic acid (H2edb) in DMF at 80 °C gave the metal–organic framework material [Zn4O(edb)3(H2O)2]·6DMF 1 in which edb ligands connect Zn4O centres into a doubly-interpenetrated cubic network with a similar topology to observed with other linear dicarboxylates in the IRMOF series. Analysis of the nitrogen isotherm revealed the material to have a BET surface area of 1088 m2 g−1, which is approximately one-third of the value calculated from GCMC simulations, suggesting incomplete activation or pore blocking in the activated material. The reaction of cobalt(II) nitrate and H2edb in DMF gave [Co3(edb)3(DMF)4]·2.6DMF 2. The structure of 2 is based on Co3(O2CR)6 linear secondary building units that are linked by the edb ligands into a two-dimensional network. When 2 was placed under vacuum, a colour change from pale pink to deep blue was observed, which is consistent with loss of the coordinated DMF molecules. When treated with [Co2(CO)8], crystals of 1 turned dark red, and IR analysis is consistent with coordination of Co2(CO)6 fragments to the alkyne groups. However, the colour change was restricted to the external crystal surfaces. This is a likely consequence of partial framework collapse, which occurs following coordination of Co2(CO)6 to the alkyne groups. Coordination changes the preferred angle between carboxylate groups in the edb ligand, which in turn introduces strain into the network

    Genetic history of Cambridgeshire before and after the Black Death.

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    The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death

    Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

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    Hansen’s disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease’s complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period

    Pathways to the medieval hospital : Collective osteobiographies of poverty and charity

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    Medieval hospitals were founded to provide charity, but poverty and infirmity were broad and socially determined categories and little is known about the residents of these institutions and the pathways that led them there. Combining skeletal, isotopic and genetic data, the authors weave a collective biography of individuals buried at the Hospital of St John the Evangelist, Cambridge. By starting with the physical remains, rather than historical expectations, they demonstrate the varied life courses of those who were ultimately buried in the hospital's cemetery, illustrating the diverse faces of medieval poverty and institutional notions of charity. The findings highlight the value of collective osteobiography when reconstructing the social landscapes of the past

    Estimating population size, density and dynamics of Pre-Pottery Neolithic villages in the central and southern Levant: an analysis of Beidha, southern Jordan

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    The Pre-Pottery Neolithic (PPN) of the central and southern Levant played an integral role in the Neolithic Demographic Transition (NDT) from mobile hunter-gatherer to village-based, agro-pastoralist societies. An understanding of population dynamics is essential for reconstructing the trajectories of these early village societies. However, few investigations have produced absolute estimates of population parameters for these villages and those which have base estimates on a limited methodological framework. This research examines the methodological and theoretical basis for existing estimates, and explores a range of methodologies in order to derive more empirically-robust demographic data. Results reveal that commonly utilized methodologies and population density coefficients employed for estimating PPN village populations require re-evaluation. This article presents the application of methodologies to the PPNB site of Beidha in southern Jordan
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