scholarly journals Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Maria A. Spyrou ◽  
Marcel Keller ◽  
Rezeda I. Tukhbatova ◽  
Christiana L. Scheib ◽  
Elizabeth A. Nelson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Eastern Europe ◽  
Yersinia Pestis ◽  
Human Remains ◽  
Genomic Region ◽  
Archaeological Sites ◽  
Black Death ◽  
Evolutionary Trajectory ◽  
Late Stages ◽  
Initial Entry

Abstract 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.

scholarly journals A phylogeography of the second plague pandemic revealed through the analysis of historical Y. pestis genomes

2018 ◽  
Author(s):  
Maria A. Spyrou ◽  
Marcel Keller ◽  
Rezeda I. Tukhbatova ◽  
Elizabeth A. Nelson ◽  
Aida Andrades Valtueňa ◽  
...  
Keyword(s):  
Early Modern ◽  
18Th Century ◽  
Genomic Region ◽  
Archaeological Sites ◽  
Black Death ◽  
Initial Wave ◽  
Low Diversity ◽  
Early Modern Era ◽  
Modern Era ◽  
Late Stages

The second plague pandemic (14th - 18th century AD), caused by the bacterium Yersinia pestis, is infamous for its initial wave, the Black Death (1346-1353 AD), and its repeated scourges in Europe and the vicinity until the Early Modern Era. Here, we report 32 ancient Y. pestis genomes spanning the 14th to 17th century AD through the analysis of human remains from nine European archaeological sites. Our data support an initial entry of the bacterium from Eastern Europe and the absence of genetic diversity during the Black Death as well as low diversity during local outbreaks thereafter. Moreover, 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. Finally, we show the loss of a genomic region that includes virulence-associated genes in strains associated with late stages of the second plague pandemic (17th - 18th century AD). This deletion could not be detected in extant strains within our modern dataset, though it was identified in a today-extinct lineage associated with the first plague pandemic (6th - 8th century AD), suggesting convergent evolution during both pandemic events.

From Black Death to Black Hole

2018 ◽  
Author(s):  
Marcin Piatkowski
Keyword(s):  
Economic Development ◽  
Black Hole ◽  
Sixteenth Century ◽  
Eastern Europe ◽  
Rule Of Law ◽  
Western Europe ◽  
Black Death ◽  
European Continent ◽  
The Past

In this chapter I explain why Poland and most countries in Eastern Europe have always lagged behind Western Europe in economic development. I discuss why in the past the European continent split into two parts and how Western and Eastern Europe followed starkly different developmental paths. I then demonstrate how Polish oligarchic elites built extractive institutions and how they adopted ideologies, cultures, and values, which undermined development from the late sixteenth century to 1939. I also describe how the elites created a libertarian country without taxes, state capacity, and rule of law, and how this ‘golden freedom’ led to Poland’s collapse and disappearance from the map of Europe in 1795. I argue that Polish extractive society was so well established that it could not reform itself from the inside. It was like a black hole, where the force of gravity is so strong that the light could not come out.

scholarly journals Recombination and Gene Conversion in a 170-kb Genomic Region of Arabidopsis thaliana

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1269-1278 ◽  
Author(s):  
Bernhard Haubold ◽  
Jürgen Kroymann ◽  
Andreas Ratzka ◽  
Thomas Mitchell-Olds ◽  
Thomas Wiehe
Keyword(s):  
Genetic Diversity ◽  
Arabidopsis Thaliana ◽  
Linkage Disequilibrium ◽  
Gene Conversion ◽  
Genomic Sequence ◽  
Genomic Region ◽  
Resistance To Herbivory ◽  
Linkage Disequilibria ◽  
Coalescent Simulations ◽  
The Mean

Abstract Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity (πs) varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent simulations and estimate that up to 90% of recombination is due to gene conversion.

Early Upper Paleolithic in Eastern Europe and Implications for the Dispersal of Modern Humans

Science ◽  
2007 ◽  
Vol 315 (5809) ◽  
pp. 223-226 ◽  
Author(s):  
M. V. Anikovich ◽  
A. A. Sinitsyn ◽  
John F. Hoffecker ◽  
Vance T. Holliday ◽  
V. V. Popov ◽  
...  
Keyword(s):  
Eastern Europe ◽  
Upper Paleolithic ◽  
Luminescence Dating ◽  
Archaeological Sites ◽  
Northern Eurasia ◽  
Modern Humans ◽  
Optically Stimulated Luminescence Dating ◽  
Figurative Art ◽  
Early Upper Paleolithic ◽  
Don River

Radiocarbon and optically stimulated luminescence dating and magnetic stratigraphy indicate Upper Paleolithic occupation—probably representing modern humans—at archaeological sites on the Don River in Russia 45,000 to 42,000 years ago. The oldest levels at Kostenki underlie a volcanic ash horizon identified as the Campanian Ignimbrite Y5 tephra that is dated elsewhere to about 40,000 years ago. The occupation layers contain bone and ivory artifacts, including possible figurative art, and fossil shells imported more than 500 kilometers. Thus, modern humans appeared on the central plain of Eastern Europe as early as anywhere else in northern Eurasia.

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.

1. Plague

2016 ◽  
pp. 7-30
Author(s):  
Christian W. McMillen
Keyword(s):  
Yersinia Pestis ◽  
Near East ◽  
Sixth Century ◽  
Black Death ◽  
Pacific World ◽  
The Third ◽  
The Pacific ◽  
New Antibiotics ◽  
Improved Sanitation

The plague is a disease caused by a bacillus, Yersinia pestis, transmitted by the bite of an infected flea. ‘Plague’ identifies three main periods of the pandemic. It first appeared in the sixth century ce with several epidemics in Europe and the Near East lasting until the end of the eight century. The second pandemic—the Black Death—began in 1347 and killed up to half of the continent’s population. The last European outbreak was in Russia in 1770. The third pandemic began in China in 1890 and spread rapidly around the Pacific world. Improved sanitation, isolation, and new antibiotics help, but the plague still exists today.

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 A draft genome of Yersinia pestis from victims of the Black Death

Nature ◽  
2011 ◽  
Vol 478 (7370) ◽  
pp. 506-510 ◽  
Author(s):  
Kirsten I. Bos ◽  
Verena J. Schuenemann ◽  
G. Brian Golding ◽  
Hernán A. Burbano ◽  
Nicholas Waglechner ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Draft Genome ◽  
Black Death
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