scholarly journals On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1628
Author(s):  
Kanika D. Nahata ◽  
Nena Bollen ◽  
Mandev S. Gill ◽  
Maylis Layan ◽  
Hervé Bourhy ◽  
...  
Keyword(s):  
Rabies Virus ◽  
Rna Viruses ◽  
Sequence Data ◽  
The Past ◽  
Research Areas ◽  
Research Fields ◽  
History Of ◽  
Review Study ◽  
Global Initiative ◽  
Reservoir Hosts

Rabies is a neglected zoonotic disease which is caused by negative strand RNA-viruses belonging to the genus Lyssavirus. Within this genus, rabies viruses circulate in a diverse set of mammalian reservoir hosts, is present worldwide, and is almost always fatal in non-vaccinated humans. Approximately 59,000 people are still estimated to die from rabies each year, leading to a global initiative to work towards the goal of zero human deaths from dog-mediated rabies by 2030, requiring scientific efforts from different research fields. The past decade has seen a much increased use of phylogeographic and phylodynamic analyses to study the evolution and spread of rabies virus. We here review published studies in these research areas, making a distinction between the geographic resolution associated with the available sequence data. We pay special attention to environmental factors that these studies found to be relevant to the spread of rabies virus. Importantly, we highlight a knowledge gap in terms of applying these methods when all required data were available but not fully exploited. We conclude with an overview of recent methodological developments that have yet to be applied in phylogeographic and phylodynamic analyses of rabies virus.

scholarly journals Making Genomic Surveillance Deliver: A Lineage Classification and Nomenclature System to Inform Rabies Virus Elimination

2021 ◽  
Author(s):  
Kathryn Campbell ◽  
Robert J Gifford ◽  
Joshua Singer ◽  
Verity Hill ◽  
Aine O'Toole ◽  
...  
Keyword(s):  
Rabies Virus ◽  
Sequence Data ◽  
Classification Systems ◽  
Virus Elimination ◽  
Data Resource ◽  
Genomic Tools ◽  
Control Programmes ◽  
History Of ◽  
Virus Sequence ◽  
Globally Distributed

The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 73 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, and areas of persistence and transmission, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as we work towards eliminating dog-mediated rabies, as well as having potential for broad application to the surveillance of other viruses.

Beyond the Big Five: Extinctions as Experiments in the History of Life

2008 ◽  
Vol 14 ◽  
pp. 249-270 ◽  
Author(s):  
Rowan Lockwood
Keyword(s):  
Mass Extinction ◽  
Interdisciplinary Approach ◽  
Future Research ◽  
Past Century ◽  
Natural Experiments ◽  
Evolutionary Patterns ◽  
The Past ◽  
Research Areas ◽  
History Of ◽  
Extinction Events

The past century has witnessed a number of significant breakthroughs in the study of extinction in the fossil record, from the discovery of a bolide impact as the probable cause of the end-Cretaceous (K/T) mass extinction to the designation of the “Big 5” mass extinction events. Here, I summarize the major themes that have emerged from the past thirty years of extinction research and highlight a number of promising directions for future research. These directions explore a central theme—the evolutionary consequences of extinction— and focus on three broad research areas: the effects of selectivity, the importance of recovery intervals, and the influence of spatial patterns. Examples of topics explored include the role that trait variation plays in survivorship, the comparative effects of extinctions of varying magnitudes on evolutionary patterns, the re-establishment of macroevolutionary patterns in the aftermath of extinction, and the extent to which spatial autocorrelation affects extinction patterns. These topics can be approached by viewing extinctions as repeated natural experiments in the history of life and developing hypotheses to explicitly test across multiple events. Exploring the effects of extinction also requires an interdisciplinary approach, applying evolutionary, ecological, geochronological, geochemical, tectonic, and paleoclimatic tools to both extinction and recovery intervals.

scholarly journals Statistical inference for the evolutionary history of cancer genomes

2019 ◽  
Author(s):  
K. N. Dinh ◽  
R. Jaksik ◽  
M. Kimmel ◽  
A. Lambert ◽  
S. Tavaré
Keyword(s):  
Sequence Data ◽  
Past History ◽  
The Cancer Genome Atlas ◽  
Death Process ◽  
Tumor Evolution ◽  
Cancer Evolution ◽  
Reverse Time ◽  
The Past ◽  
History Of ◽  
Birth Death

AbstractRecent years have produced a large amount of work on inference about cancer evolution from mutations identified in cancer samples. Much of the modeling work has been based on classical models of population genetics, generalized to accommodate time-varying cell population size. Reverse-time genealogical views of such models, commonly known as coalescents, have been used to infer aspects of the past of growing populations. Another approach is to use branching processes, the simplest scenario being the linear birth-death process (lbdp), a binary fission Markov age-dependent branching process. A genealogical view of such models is also available. The two approaches lead to similar but not identical results. Inference from evolutionary models of DNA often exploits summary statistics of the sequence data, a common one being the so-called Site Frequency Spectrum (SFS). In a sequencing experiment with a known number of sequences, we can estimate for each site at which a novel somatic mutation has arisen, the number of cells that carry that mutation. These numbers are then grouped into sites which have the same number of copies of the mutant. SFS can be computed from the statistics of mutations in a sample of cells, in which DNA has been sequenced. In this paper, examine how the SFS based on birth-death processes differ from those based on the coalescent model. This may stem from the different sampling mechanisms in the two approaches. However, we also show mathematically and computationally that despite this, they can be made quantitatively comparable at least for the range of parameters typical for tumor cell populations. We also present a model of tumor evolution with selective sweeps, based on coalescence, and demonstrate how it may help in understanding the past history of tumor as well the influence of data pre-processing. We illustrate the theory with applications to several examples of The Cancer Genome Atlas tumors.

scholarly journals Early history of Neanderthals and Denisovans

2017 ◽  
Vol 114 (37) ◽  
pp. 9859-9863 ◽  
Author(s):  
Alan R. Rogers ◽  
Ryan J. Bohlender ◽  
Chad D. Huff
Keyword(s):  
Gene Flow ◽  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Early History ◽  
Middle Pleistocene ◽  
Dna Sequence Data ◽  
The Past ◽  
History Of

Extensive DNA sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. We introduce a method to study the past several hundred thousand years. Our results show that (i) the Neanderthal–Denisovan lineage declined to a small size just after separating from the modern lineage, (ii) Neanderthals and Denisovans separated soon thereafter, and (iii) the subsequent Neanderthal population was large and deeply subdivided. They also (iv) support previous estimates of gene flow from Neanderthals into modern Eurasians. These results suggest an archaic human diaspora early in the Middle Pleistocene.

scholarly journals Problematyka naukowo-badawcza i dorobek naukowy pracowników Katedry Pedagogiki i Dydaktyki Uniwersytetu Poznańskiego 1919–1939 w stulecie powstania Uniwersytetu im. Adama Mickiewicza w Poznaniu (1919–2019)

1970 ◽  
pp. 145-165
Author(s):  
Konrad Nowak-Kluczyński
Keyword(s):  
Interwar Period ◽  
Research Issues ◽  
Academic Achievements ◽  
Research Areas ◽  
Research Fields ◽  
National Trend ◽  
History Of ◽  
Dynamic Research ◽  
Adam Mickiewicz

Research issues and academic achievements of the faculty of the Department of Pedagogy and Teaching at Poznań University in 1919–1939 on the centennial of the establishment of Adam Mickiewicz University in Poznań (1919–2019). In its early days, Poznań University attracted a large number of researchers representing many disciplines of science but prevailing humanities. Poznań was a centre of very dynamic research into pedagogy and psychology. Initially, the Department of Pedagogy and Teaching at Poznań University focused on just a few research fields and areas. In the lead were issues related to the theory of upbringing, educating adults and the history of upbringing. In the local Department of Pedagogy and Teaching, a number of contributions was made to teaching and the methodology of some teaching subjects. In the Interwar Period, the following research areas were pursued by the pedagogy teachers at Poznań University: Antoni Danysz’ progressive-national trend referring to the ideological traditions of the Revolutions of 1848; Ludwik Jaxa-Bykowski’s nationalist-anthropological trend resulting from nationalist conflicts and efforts to reinforce the nation with special emphasis placed on the first decade of Poland’s independence; Marian Wachowski’s nationalist-imperialistic trend based on German philosophical pedagogy.

Polin: Studies in Polish Jewry Volume 33

2021 ◽  
Keyword(s):  
Religious Life ◽  
Sociology Of Religion ◽  
Religious Practice ◽  
Beliefs And Practices ◽  
The Past ◽  
Research Areas ◽  
History Of ◽  
Material History ◽  
Source Materials

Following tremendous advances in recent years in the study of religious belief, this volume adopts a fresh understanding of Jewish religious life in Poland. Approaches deriving from the anthropology, history, phenomenology, psychology, and sociology of religion have replaced the methodologies of social or political history that were applied in the past, offering fascinating new perspectives. The well-established interest in Hasidism continues, albeit from new angles, but topics that have barely been considered before are well represented here too. Women’s religious practice gains new prominence, and a focus on elites has given way to a consideration of the beliefs and practices of ordinary people. Reappraisals of religious responses to secularization and modernity, both liberal and Orthodox, offer more nuanced insights into this key issue. Other research areas represented here include the material history of Jewish religious life in eastern Europe and the shift of emphasis from theology to praxis in the search for the defining quality of religious experience. The contemporary reassessments in this volume, with their awareness of emerging techniques that have the potential to extract fresh insights from source materials both old and new, show how our understanding of what it means to be Jewish is continuing to expand.

scholarly journals One Year of SARS-CoV-2: How Much Has the Virus Changed?

Biology ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 91
Author(s):  
Santiago Vilar ◽  
Daniel G. Isom
Keyword(s):  
Public Health ◽  
Viral Genome ◽  
Sequence Data ◽  
Viral Proteins ◽  
Mutation Rates ◽  
Research Groups ◽  
Site Specific ◽  
The Past ◽  
Global Initiative ◽  
One Year

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide crisis with profound effects on both public health and the economy. In order to combat the COVID-19 pandemic, research groups have shared viral genome sequence data through the Global Initiative on Sharing All Influenza Data (GISAID). Over the past year, ≈290,000 full SARS-CoV-2 proteome sequences have been deposited in the GISAID. Here, we used these sequences to assess the rate of nonsynonymous mutants over the entire viral proteome. Our analysis shows that SARS-CoV-2 proteins are mutating at substantially different rates, with most of the viral proteins exhibiting little mutational variability. As anticipated, our calculations capture previously reported mutations that arose in the first months of the pandemic, such as D614G (Spike), P323L (NSP12), and R203K/G204R (Nucleocapsid), but they also identify more recent mutations, such as A222V and L18F (Spike) and A220V (Nucleocapsid), among others. Our comprehensive temporal and geographical analyses show two distinct periods with different proteome mutation rates: December 2019 to July 2020 and August to December 2020. Notably, some mutation rates differ by geography, primarily during the latter half of 2020 in Europe. Furthermore, our structure-based molecular analysis provides an exhaustive assessment of SARS-CoV-2 mutation rates in the context of the current set of 3D structures available for SARS-CoV-2 proteins. This emerging sequence-to-structure insight is beginning to illuminate the site-specific mutational (in)tolerance of SARS-CoV-2 proteins as the virus continues to spread around the globe.

On The Possibility of an Autonomous History of Modern Southeast Asia

1961 ◽  
Vol 2 (2) ◽  
pp. 73-105 ◽  
Author(s):  
John R. W. Small
Keyword(s):  
Southeast Asia ◽  
Contemporary History ◽  
The Past ◽  
History Of

It is generally accepted that history is an element of culture and the historian a member of society, thus, in Croce's aphorism, that the only true history is contemporary history. It follows from this that when there occur great changes in the contemporary scene, there must also be great changes in historiography, that the vision not merely of the present but also of the past must change.

Stellar Evolution

1962 ◽  
Vol 11 (02) ◽  
pp. 137-143
Author(s):  
M. Schwarzschild
Keyword(s):  
Solar System ◽  
Stellar Evolution ◽  
Space Craft ◽  
New Techniques ◽  
Substantial Body ◽  
Individual Stars ◽  
The Past ◽  
Evolution Of Galaxies ◽  
History Of ◽  
Fast Flow

It is perhaps one of the most important characteristics of the past decade in astronomy that the evolution of some major classes of astronomical objects has become accessible to detailed research. The theory of the evolution of individual stars has developed into a substantial body of quantitative investigations. The evolution of galaxies, particularly of our own, has clearly become a subject for serious research. Even the history of the solar system, this close-by intriguing puzzle, may soon make the transition from being a subject of speculation to being a subject of detailed study in view of the fast flow of new data obtained with new techniques, including space-craft.

A 200-Year History of the Study of Childhood Language Disorders of Unknown Origin: Changes in Terminology

2020 ◽  
Vol 5 (1) ◽  
pp. 6-11 ◽  
Author(s):  
Laurence B. Leonard
Keyword(s):  
Language Impairment ◽  
Specific Language Impairment ◽  
Scientific Literature ◽  
Language Disorder ◽  
Language Disorders ◽  
Unknown Origin ◽  
Developmental Language Disorder ◽  
The Past ◽  
History Of ◽  
The Many

Purpose The current “specific language impairment” and “developmental language disorder” discussion might lead to important changes in how we refer to children with language disorders of unknown origin. The field has seen other changes in terminology. This article reviews many of these changes. Method A literature review of previous clinical labels was conducted, and possible reasons for the changes in labels were identified. Results References to children with significant yet unexplained deficits in language ability have been part of the scientific literature since, at least, the early 1800s. Terms have changed from those with a neurological emphasis to those that do not imply a cause for the language disorder. Diagnostic criteria have become more explicit but have become, at certain points, too narrow to represent the wider range of children with language disorders of unknown origin. Conclusions The field was not well served by the many changes in terminology that have transpired in the past. A new label at this point must be accompanied by strong efforts to recruit its adoption by clinical speech-language pathologists and the general public.

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