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

2019 ◽  
Vol 116 (25) ◽  
pp. 12363-12372 ◽  
Author(s):  
Marcel Keller ◽  
Maria A. Spyrou ◽  
Christiana L. Scheib ◽  
Gunnar U. Neumann ◽  
Andreas Kröpelin ◽  
...  
Keyword(s):  
Roman Empire ◽  
Yersinia Pestis ◽  
Western Europe ◽  
18Th Century ◽  
Methodological Approach ◽  
Genomic Region ◽  
Nucleotide Polymorphisms ◽  
Early Diversification ◽  
Pandemic Strains ◽  
Low Coverage

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.

scholarly journals AncientYersinia pestisgenomes from across Western Europe reveal early diversification during the First Pandemic (541–750)

2018 ◽  
Author(s):  
Marcel Keller ◽  
Maria A. Spyrou ◽  
Christiana L. Scheib ◽  
Andreas Kröpelin ◽  
Brigitte Haas-Gebhard ◽  
...  
Keyword(s):  
Roman Empire ◽  
Yersinia Pestis ◽  
Virulence Factors ◽  
Large Scale ◽  
Western Europe ◽  
Methodological Approach ◽  
Genomic Region ◽  
Early Medieval Period ◽  
Early Diversification ◽  
Genome Decay

AbstractThe first historically documented pandemic caused byYersinia pestisstarted as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although palaeogenomic studies have previously identified the causative agent asY. 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 20 sites in Austria, Britain, Germany, France and Spain forY. pestisDNA and reconstructed six new genomes. We present a novel methodological approach assessing SNPs in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis reveals the existence of previously undocumentedY. pestisdiversity during the 6th–7thcenturies, and provides evidence for the presence of multiple distinctY. pestisstrains 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 southern France and Spain, and that southern Germany seems to have been affected by at least two distinctY. pestisstrains. Four of the reported strains form a polytomy similar to others seen across theY. pestisphylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45 kb genomic region in the most recent First Pandemic strain affecting two virulence factors, intriguingly overlapping with a deletion found in 17th–18th-century genomes of the Second Pandemic.Significance StatementThe first historically reported pandemic attributed toYersinia pestisstarted with the Justinianic Plague (541–544) and continued for around 200 years as the so-called First Pandemic. To date, only oneY. pestisstrain from this pandemic has been reconstructed using ancient DNA. In this study, we present six new genomes from Britain, France, Germany and Spain, demonstrating the geographic range of plague during the First pandemic and showing microdiversity in the Early Medieval Period. Moreover, we detect similar genome decay during the First and Second Pandemic (17thto 18thcentury) that includes the same two virulence factors, thus providing an example of potential convergent evolution ofY. pestisduring large scale epidemics.

scholarly journals Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Archana Khadgi ◽  
Courtney A. Weber
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Rubus Idaeus ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Red Raspberry ◽  
Genome Wide ◽  
A Genome ◽  
Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

scholarly journals Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xingyi Wang ◽  
Hui Liu ◽  
Kadambot H. M. Siddique ◽  
Guijun Yan
Keyword(s):  
Candidate Genes ◽  
Quantitative Trait ◽  
Genomic Region ◽  
Nucleotide Polymorphisms ◽  
Near Isogenic Lines ◽  
Gene Effects ◽  
Isogenic Lines ◽  
Trait Locus ◽  
Grain Yield And Quality ◽  
Sprouting Resistance

Abstract Background Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL) QPhs.ccsu-3A.1 for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated. Results Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlie QPhs.ccsu-3A.1 responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines. Conclusions The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.

Austria inventa?

2020 ◽  
Author(s):  
Martin P. Schennach
Keyword(s):  
Roman Empire ◽  
Constitutional Law ◽  
18Th Century ◽  
Holy Roman Empire ◽  
Historical Research ◽  
University Teaching ◽  
Legal Construction ◽  
Internal Integration ◽  
The One ◽  
State Rights

This is the first work of its kind devoted to Austrian constitutional law, which has so far received little attention in (legal) historical research. It examines its origins, its authors, its connection with the “Reichspublizistik”, its sources and methods as well as its contents and, last but not least, its role in university teaching. Of all the particular state rights in the Holy Roman Empire, its subject was probably the one most intensively discussed. In the second half of the 18th century, Austrian constitutional law was a flourishing genre of literature promoted by the Habsburg dynasty. This is accounted for by its main themes: It flanked the process of internal integration of the heterogeneous Habsburg ruling complex and aimed at the discursive and legal construction of an Austrian state as a whole and the legitimation of absolutism.

Jauna slota tīri slauka jeb muižnieka Bernharda Magnusa fon Vulfa tiesas prāva pret mācītāju Frīdrihu Danielu Vāru

2021 ◽  
pp. 122-136
Author(s):  
Ginta Pērle-Sīle
Keyword(s):  
Western Europe ◽  
18Th Century ◽  
Contextual Information ◽  
Social Groups ◽  
Literary Work ◽  
Court Case ◽  
Political Events ◽  
The One ◽  
The Relationship ◽  
Research Show

The subject of this article is a court case between Aumeisteri nobleman Berhard Magnus von Wulf (1732–1784) and the minister of Palsmane and Aumeisteri parishes Friedrich Daniel Wahr (1749–1827) about the suspension of the minister from his duties from 1775 to 1779. The aim of the research is to approach the court case as evidence of the different opinions of several social groups where extreme colonial ideas in Vidzeme meet Enlightenment ideas from Western Europe. At the same time, the court case is a source of contextual information for a better understanding of the development of Wahr’s literary and folkloristic heritage. The research is based on studies of documents found in the Latvian State History Archive that are approached using the culture-historical and comparative methods, thus trying to contextualize certain events in a specific place and time. The results of the research show the Palsmane and Aumeisteri society as typical of the second part of the 18th century. The existence of specific social groups, particularism, and the implementation of colonial attitudes by the local nobility are also evident. The attitude of Wahr towards Latvian peasants shows the influence of Enlightenment, especially his efforts in education. The relationship between the parish and its minister incorporates evidence of a syncretic praxis with pagan and Christian traditions. In the light of political events of that particular time, i. e. peasant rebels in Vidzeme, the court case allows Wulf’s accusations to be treated as an opportunity to decrease the implementation of Enlightenment ideas, thus safeguarding the local nobility’s power. At the same time, the court case is a source of biographic, private, and daily life details. The broad range of the parish territory which was often challenging to navigate, the modest means of the minister, and distancing of the local nobility on the one hand, along with the influence of enlightenment ideas, on the other hand, are the most probable grounding for Wahr’s folkloristic and literary work.

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

2018 ◽  
Vol 115 (50) ◽  
pp. E11790-E11797 ◽  
Author(s):  
Amine Namouchi ◽  
Meriam Guellil ◽  
Oliver Kersten ◽  
Stephanie Hänsch ◽  
Claudio Ottoni ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Evolutionary History ◽  
18Th Century ◽  
Human Movement ◽  
Integrative Approach ◽  
Medieval Period ◽  
Trade Routes ◽  
Historical Landscape ◽  
Genomic Studies ◽  
History Of

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.

scholarly journals Genetic Diversity, Structure, and Selective Sweeps in Spinacia turkestanica Associated With the Domestication of Cultivated Spinach

2021 ◽  
Vol 12 ◽  
Author(s):  
Sanjaya Gyawali ◽  
Gehendra Bhattarai ◽  
Ainong Shi ◽  
Chris Kik ◽  
Lindsey J. du Toit
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Selective Sweep ◽  
Spinacia Oleracea ◽  
Genomic Region ◽  
Day Length ◽  
Mountain Range ◽  
Nucleotide Polymorphisms ◽  
Selective Sweeps ◽  
Genetic Diversity And Structure

Genotype-by-sequencing (GBS) was used to explore the genetic diversity and structure of Spinacia turkestanica, and the selective sweeps involved in domestication of cultivated spinach, S. oleracea, from S. turkestanica. A total 7,065 single nucleotide polymorphisms (SNPs) generated for 16 Spinacia oleracea and 76 S. turkestanica accessions placed the S. oleracea accessions in one group, Q1, and the 76 S. turkestanica accessions, which originated from Central Asia, in two distinct groups, Q2 and Q3. The Q2 group shared greater genetic identity with the S. oleracea accessions, Q1, than the Q3 S. turkestanica group. Likewise, the S. oleracea Q1 group had a smaller Fst (0.008) with the Q2 group than with the Q3 group (Fst = 0.012), and a greater gene flow (Nm = 30.13) with the Q2 group than with the Q3 group (Nm = 21.83). The Q2 accessions originated primarily from Uzbekistan while the Q3 accessions originated mostly from Tajikistan. The Zarafshan Mountain Range appears to have served as a physical barrier that largely separated members of the Q2 and Q3 groups of S. turkestanica. Accessions with admixtures of Q2 and Q3 were collected primarily from lower elevations at the southern end of the Zarafshan Mountain Range in Uzbekistan. Selective sweep regions identified at 32, 49, and 52 Mb on chromosomes 1, 2, and 3, respectively, appear to have played a vital role in the domestication of S. oleracea as they are correlated with important domestication traits, including day length sensitivity for bolting (flowering). High XP-CLR scores at the 52 Mb genomic region of chromosome three suggest that a selective sweep at this region was responsible for early differentiation of S. turkestanica into two groups in Central Asia.

scholarly journals Wesley in Oxford and the Legend of Holy Grail’s Knight: The Study about the Root of Methodism to the World, and the Foundation of Kwansei-Gakuin in Japan

2017 ◽  
Vol 6 (1) ◽  
pp. 9-16
Author(s):  
Kawanishi Takao
Keyword(s):  
Roman Empire ◽  
19Th Century ◽  
18Th Century ◽  
Round Table ◽  
King Arthur ◽  
Spiritual Power ◽  
The World ◽  
Methodist Episcopal Church ◽  
New States ◽  
The 19Th Century

Abstract John Wesley (1703-91）is known as the founder of Methodism in his time of Oxford University’s Scholar. However, about his Methodical religious theory, he got more spiritual and important influence from other continents not only Oxford in Great Britain but also Europe and America. Through Wesley’s experience and awakening in those continents, Methodism became the new religion with Revival by the spiritual power of “Holy Grail”. By this research using Multidisciplinary approach about the study of Legend of Holy Grail’s Knight, - from King Arthur and Knights of the Round Table in the Medieval Period, and in 18th century Wesley, who went to America in the way on ship where he met the Moravian Church group also called Herrnhut having root of Pietisms, got important impression in his life. After this awakening, he went to meet Herrnhut supervisor Zinzendorf (1700-60) in Germany who had root of a noble house in the Holy Roman Empire, - and to Legend of Holy Grail’s Knight Opera “Parsifal” by Richard Wagner at Bayreuth near Herrnhut’s land in the 19th century, Wesley’s Methodism is able to reach new states with the legend, such as the historical meaning of Christianity not only Protestantism but also Catholicism. I wish to point out Wesley’s Methodism has very close to Legend of Holy Grail’s Knight. In addition, after the circulation in America, in the late 19th century Methodism spread toward Africa, and Asian Continents. Especially in Japan, by Methodist Episcopal Church South, Methodism landed in the Kansai-area such international port city Kobe. Methodist missionary Walter Russel Lambuth (1854-1921) who entered into Japan founded English schools to do his missionary works. Afterward, one of them became Kwansei-Gakuin University in Kobe. Moreover, Lambuth such as Parsifal with Wesley’s theories went around the world to spread Methodism with the Spirit’s the Legend of Holy Grail’s Knight as World Citizen.

scholarly journals Meatscapes: Spaces and processes associated to subsistence livestock

2016 ◽  
Vol 7 (2) ◽  
Author(s):  
Leila Marie Farah
Keyword(s):  
Urban Development ◽  
18Th Century ◽  
Methodological Approach ◽  
Analytical Framework ◽  
Urban Landscapes ◽  
Historical Maps ◽  
Legal Documents ◽  
New Perspective ◽  
Livestock Products ◽  
By Products

How was subsistence livestock linked to architecture and the urban development in the settlement of 17th and 18th century Montreal? This article argues that landscapes and buildings interact with and accommodate the transformation of livestock products and by-products along various stages; and, that these animal parts contribute to defining urban landscapes. The paper presents a novel analytical framework to study foodscapes, and more particularly meatscapes by way of identifying spaces through which animal parts transited, and by spatially mapping them. It does so via a mixed methodological approach, including researching legal documents, travelers’ notes, databases, historical maps and plans dating back to the French period. Examining processes and spaces involving subsistence livestock, their products and by-products as well as individuals related to their transformation provides a new perspective on how ordinary activities shaped the lives and the spaces in a settlement.

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