scholarly journals Fundamental Difficulties Prevent the Reconstruction of the Deep Phylogeny of Viruses

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1130 ◽  
Author(s):  
Jean-Michel Claverie
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Environmental Virology ◽  
Fundamental Limitations ◽  
Intracellular Parasites ◽  
Virion Structure ◽  
Agricultural Applications ◽  
History Of ◽  
High Level ◽  
Biological Entities

The extension of virology beyond its traditional medical, veterinary, or agricultural applications, now called environmental virology, has shown that viruses are both the most numerous and diverse biological entities on Earth. In particular, virus isolations from unicellular eukaryotic hosts (heterotrophic and photosynthetic protozoans) revealed numerous viral types previously unexpected in terms of virion structure, gene content, or mode of replication. Complemented by large-scale metagenomic analyses, these discoveries have rekindled interest in the enigma of the origin of viruses, for which a description encompassing all their diversity remains not available. Several laboratories have repeatedly tackled the deep reconstruction of the evolutionary history of viruses, using various methods of molecular phylogeny applied to the few shared “core” genes detected in certain virus groups (e.g., the Nucleocytoviricota). Beyond the practical difficulties of establishing reliable homology relationships from extremely divergent sequences, I present here conceptual arguments highlighting several fundamental limitations plaguing the reconstruction of the deep evolutionary history of viruses, and even more the identification of their unique or multiple origin(s). These arguments also underline the risk of establishing premature high level viral taxonomic classifications. Those limitations are direct consequences of the random mechanisms governing the reductive/retrogressive evolution of all obligate intracellular parasites.

ARENA

2021 ◽  
pp. 126-165
Author(s):  
James Loxton
Keyword(s):  
Large Scale ◽  
Right Wing ◽  
Left Wing ◽  
Military Rule ◽  
Death Squad ◽  
Powerful Source ◽  
Fourth Section ◽  
The Third ◽  
History Of ◽  
High Level

This chapter examines ARENA in El Salvador and argues that, like the UDI in Chile, its success was the product of authoritarian inheritance and counterrevolutionary struggle. The first section discusses El Salvador’s long history of right-wing military rule. The second section examines the October 1979 coup and the resulting establishment of a left-wing Revolutionary Governing Junta. The third section discusses the intense counterrevolutionary response that the junta triggered. This included large-scale death squad violence, with future ARENA founder Roberto D’Aubuisson playing a key role. The fourth section examines the formation of ARENA in response to an impending transition to competitive elections. The fifth section shows how D’Aubuisson’s role as a high-level official in the pre-1979 military regime endowed ARENA with several valuable resources. The final section discusses how ARENA’s origins in counterrevolutionary struggle served as a powerful source of cohesion.

scholarly journals RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics

IMA Fungus ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yi Li ◽  
Lan Jiang ◽  
Ke Wang ◽  
Hai-Jun Wu ◽  
Rui-Heng Yang ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Its Region ◽  
Wide Distribution ◽  
Specific Primers ◽  
Ophiocordyceps Sinensis ◽  
Single Genome ◽  
History Of ◽  
Geographic Populations ◽  
Internal Transcribed Spacer Sequences

Abstract Different hypotheses have been proposed to interpret the observed unusual ITS (internal transcribed spacer) sequences in Ophiocordyceps sinensis. The coexistence of diverged ITS paralogs in a single genome was previously shown by amplifying the ITS region from mono-ascospore isolates using specific primers designed for different ITS paralog groups. Among those paralogs, are AT-biased ITS sequences which were hypothesized to result from repeat-induced point mutation (RIP). This is a process that detects and mutates repetitive DNA and frequently leads to epigenetic silencing, and these mutations have been interpreted as pseudogenes. Here we investigate the occurrence and frequency of ITS pseudogenes in populations of O. sinensis using large-scale sampling, and discusses the implications of ITS pseudogenes for fungal phylogenetic and evolutionary studies. Our results demonstrate a wide distribution of ITS pseudogenes amongst different geographic populations, and indicate how ITS pseudogenes can contribute to the reconstruction of the evolutionary history of the species.

scholarly journals Shedding new light on opsin evolution

2011 ◽  
Vol 279 (1726) ◽  
pp. 3-14 ◽  
Author(s):  
Megan L. Porter ◽  
Joseph R. Blasic ◽  
Michael J. Bok ◽  
Evan G. Cameron ◽  
Thomas Pringle ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Current Model ◽  
Expression Patterns ◽  
Model Organisms ◽  
Biological Functions ◽  
Site Specific ◽  
History Of ◽  
Functional Features

Opsin proteins are essential molecules in mediating the ability of animals to detect and use light for diverse biological functions. Therefore, understanding the evolutionary history of opsins is key to understanding the evolution of light detection and photoreception in animals. As genomic data have appeared and rapidly expanded in quantity, it has become possible to analyse opsins that functionally and histologically are less well characterized, and thus to examine opsin evolution strictly from a genetic perspective. We have incorporated these new data into a large-scale, genome-based analysis of opsin evolution. We use an extensive phylogeny of currently known opsin sequence diversity as a foundation for examining the evolutionary distributions of key functional features within the opsin clade. This new analysis illustrates the lability of opsin protein-expression patterns, site-specific functionality (i.e. counterion position) and G-protein binding interactions. Further, it demonstrates the limitations of current model organisms, and highlights the need for further characterization of many of the opsin sequence groups with unknown function.

Implementation of Paul Revere: Tough as Nails, an Integrated Project-Based Course on Materials Science and History of Technology

2004 ◽  
Vol 827 ◽  
Author(s):  
Jonathan Stolk ◽  
Robert Martello ◽  
Franklin W. Olin
Keyword(s):  
Student Satisfaction ◽  
Large Scale ◽  
Materials Science ◽  
History Of Technology ◽  
Technical Content ◽  
Hands On ◽  
History Of ◽  
Social Environmental ◽  
High Level ◽  
College Sophomores

AbstractOlin College sophomores participate in integrated course blocks that merge technical content with business, arts, humanities, and social science topics, allowing students to work on engineering projects that have broader implications than the purely technical. In this paper, we present Paul Revere: Tough as Nails, a multidisciplinary course block that combines an introductory materials science course with a history of technology course and a large scale project. In Paul Revere, students explore connections between historical and technological materials science developments through examinations of Paul Revere's metallurgical work and analyses of the relevant social, environmental, political, and economic aspects that contribute to ancient and modern technologies. The explicit linkages among technical, non-technical, and hands-on aspects of the course improve learning of traditional topics, help drive interdisciplinary thinking, and lead to a high level of student satisfaction and motivation throughout the semester.

scholarly journals Deep time diversity and the early radiations of birds

2021 ◽  
Vol 118 (10) ◽  
pp. e2019865118
Author(s):  
Yilun Yu ◽  
Chi Zhang ◽  
Xing Xu
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Evolutionary Rate ◽  
Rapid Evolution ◽  
Morphological Data ◽  
Deep Time ◽  
The Third ◽  
Time Diversity ◽  
History Of

Reconstructing the history of biodiversity has been hindered by often-separate analyses of stem and crown groups of the clades in question that are not easily understood within the same unified evolutionary framework. Here, we investigate the evolutionary history of birds by analyzing three supertrees that combine published phylogenies of both stem and crown birds. Our analyses reveal three distinct large-scale increases in the diversification rate across bird evolutionary history. The first increase, which began between 160 and 170 Ma and reached its peak between 130 and 135 Ma, corresponds to an accelerated morphological evolutionary rate associated with the locomotory systems among early stem birds. This radiation resulted in morphospace occupation that is larger and different from their close dinosaurian relatives, demonstrating the occurrence of a radiation among early stem birds. The second increase, which started ∼90 Ma and reached its peak between 65 and 55 Ma, is associated with rapid evolution of the cranial skeleton among early crown birds, driven differently from the first radiation. The third increase, which occurred after ∼40 to 45 Ma, has yet to be supported by quantitative morphological data but gains some support from the fossil record. Our analyses indicate that the bird biodiversity evolution was influenced mainly by long-term climatic changes and also by major paleobiological events such as the Cretaceous–Paleogene (K–Pg) extinction.

scholarly journals Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts

2016 ◽  
Vol 12 (12) ◽  
pp. e1006041 ◽  
Author(s):  
Cécile Troupin ◽  
Laurent Dacheux ◽  
Marion Tanguy ◽  
Claude Sabeta ◽  
Hervé Blanc ◽  
...  
Keyword(s):  
Rabies Virus ◽  
Evolutionary History ◽  
Large Scale ◽  
Phylogenomic Analysis ◽  
History Of ◽  
Complex Evolutionary History

scholarly journals Persistence and invasiveness of high-level heteroplasmy through biparental transmission of a selfish mitochondrion in Drosophila

2020 ◽  
Author(s):  
Guilherme C. Baião ◽  
Anton Strunov ◽  
Eleanor Heyworth ◽  
Daniela I. Schneider ◽  
Julia Thoma ◽  
...  
Keyword(s):  
Species Complex ◽  
Evolutionary History ◽  
High Titer ◽  
Genomic Integrity ◽  
Male And Female ◽  
Low Level ◽  
Nuclear Background ◽  
History Of ◽  
High Level ◽  
Drosophila Paulistorum

ABSTRACTHeteroplasmy is the coexistence of more than one type of mitochondria in an organism. Although widespread sequencing has identified several cases of transient or low-level heteroplasmy that primarily occur through mutation or paternal leakage, stable, high-titer heteroplasmy remains rare in animals. In this study we present a unique, stable and high-level heteroplasmy in male and female flies belonging to the neotropical Drosophila paulistorum species complex. We show that mitochondria of D. paulistorum are polyphyletic and form two clades, α and β, with two subclades each. Mitochondria of the α2 subclade appear functional based on their genomic integrity but are exclusively found in heteroplasmic flies and never in homoplasmy, suggesting that they are a secondary mitotype with distinct functionality from the primary mitochondria. Using qPCR, we show that α2 titer do not respond to energetic demands of the cell and are generally higher in males than females. By crossing hetero- and homoplasmic flies, we find that α2 can be transmitted to their offspring via both parents and that levels are dependent on nuclear background. Following α2 mitotype levels during embryogenesis, we demonstrate that this secondary mitotype replicates rapidly just after fertilization of the egg in a period when primary mitochondria are dormant. This so-called “Replication precox” mitochondrial phenotype likely prevents the α2 mitotype from being outcompeted by the primary mitotype – and thereby secures its persistence and further spread as a selfish mitochondrion, we hereby designate “Spartacus”. Finally, we reconstruct the evolutionary history of mitochondria in the willistoni subgroup uncovering signs of multiple mitochondrial losses and introgressions. Our data indicate an α-like mitochondrial ancestor in the willistoni subgroup, with the β mitotype likely acquired via introgression from an unidentified donor. We hypothesize that the selfish characteristics of α2 might have emerged as a response to competition for inheritance with the introgressed β mitotype.

scholarly journals IVAN BOBERSKYI'S CONTRIBUTION TO THE PREPARATION AND REALIZATION OF THE SHEVCHENKO CONGRESS, 1914 IN LVIV

2018 ◽  
Vol 31 ◽  
pp. 145-155
Author(s):  
Andrii SOVA
Keyword(s):  
World War I ◽  
Interwar Period ◽  
Large Scale ◽  
Political Activity ◽  
National Consciousness ◽  
World War ◽  
100Th Birthday ◽  
Sports Events ◽  
History Of ◽  
High Level

The article deals with the Shevchenkivskyi congress (other names – II Region congress, Great Memorable Shevchenkivskiy congress, Shevchenko's Jubilee congress, etc.), which took place in Lviv during June 27–29, 1914, on the occasion of the 100th birthday of Taras Shevchenko. The features of the organization and implementation of the congress, the contribution of the head of the Ukrainian gymnastic society «Sokol-Father» Ivan Boberskyi to this task were explored. The author draws attention to the fact that until 1914, Ukrainian «Sokol» and other Galicia companies did not carry out such large-scale events. It was cleared up the value of the congress in the development of national gymnastics and sports, which became the demonstration of a high-level national consciousness and dignity of the Ukrainians, a symbolic national association and a demonstration of political activity. Ivan Boberskyi did everything possible not only for the development of the Ukrainian community «Sokol» on the Ukrainian ethnic lands but also in the diaspora, the association with the Sich centers of Galicia, as well as for the consolidation of the Ukrainian nation. In the history of Galicia and in general the history of Ukraine, the Shevchenkivskiy congress, 1914 in Lviv remains one of the greatest cultural, social, political and sports events of the Galician Ukrainians in the XX century. After its successful conduction, Ivan Boberskyi in 1919 planned to hold the III Region Congress in Lviv. However, the events of World War I and the Ukrainian National Revolution of 1917–1923 prevented this. The prospects for further studies are to examine the course and results of the III Region congress, 1934, and the participation of the Ukrainian organizations in the All-Sokol congress in Prague during the interwar period. Keywords Ivan Boberskyi, Galicia, Lviv, Shevchenkivskyi congress, consolidation of Ukrainians.

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