scholarly journals An Evolving View of Phylogenetic Support

2020 ◽  
Author(s):  
Chris Simon
Keyword(s):  
Information Content ◽  
Phylogenetic Trees ◽  
Bayes Factors ◽  
Equal Proportion ◽  
Posterior Probabilities ◽  
Historical Essay ◽  
Significant Events ◽  
Branch Support ◽  
History Of ◽  
Tree Building

Abstract If all nucleotide sites evolved at the same rate within molecules and throughout the history of lineages, if all nucleotides were in equal proportion, if any nucleotide or amino acid evolved to any other with equal probability, if all taxa could be sampled, if diversification happened at well-spaced intervals, and if all gene segments had the same history, then tree building would be easy. But of course, none of those conditions are true. Hence, the need for evaluating the information content and accuracy of phylogenetic trees. The symposium for which this historical essay and presentation were developed focused on the importance of phylogenetic support, specifically branch support for individual clades. Here, I present a timeline and review significant events in the history of systematics that set the stage for the development of the sophisticated measures of branch support and examinations of the information content of data highlighted in this symposium. [Bayes factors; bootstrap; branch support; concordance factors; internode certainty; posterior probabilities; spectral analysis; transfer bootstrap expectation.]

Analyzing the Phylogenetic Trees with Tree- building Methods

2011 ◽  
Vol 1 (7) ◽  
pp. 83-85
Author(s):  
Jasmine Jasmine ◽  
◽  
Pankaj Bhambri ◽  
Dr. O.P. Gupta Dr. O.P. Gupta
Keyword(s):  
Phylogenetic Trees ◽  
Tree Building ◽  
Building Methods

scholarly journals PathFinder: Bayesian inference of clone migration histories in cancer

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i675-i683
Author(s):  
Sudhir Kumar ◽  
Antonia Chroni ◽  
Koichiro Tamura ◽  
Maxwell Sanderford ◽  
Olumide Oladeinde ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Cancer Cells ◽  
Bayesian Approach ◽  
Genetic Variants ◽  
Cancer Development ◽  
Posterior Probabilities ◽  
Migration Routes ◽  
Primary Tumors ◽  
History Of ◽  
The Web

Abstract Summary Metastases cause a vast majority of cancer morbidity and mortality. Metastatic clones are formed by dispersal of cancer cells to secondary tissues, and are not medically detected or visible until later stages of cancer development. Clone phylogenies within patients provide a means of tracing the otherwise inaccessible dynamic history of migrations of cancer cells. Here, we present a new Bayesian approach, PathFinder, for reconstructing the routes of cancer cell migrations. PathFinder uses the clone phylogeny, the number of mutational differences among clones, and the information on the presence and absence of observed clones in primary and metastatic tumors. By analyzing simulated datasets, we found that PathFinder performes well in reconstructing clone migrations from the primary tumor to new metastases as well as between metastases. It was more challenging to trace migrations from metastases back to primary tumors. We found that a vast majority of errors can be corrected by sampling more clones per tumor, and by increasing the number of genetic variants assayed per clone. We also identified situations in which phylogenetic approaches alone are not sufficient to reconstruct migration routes. In conclusion, we anticipate that the use of PathFinder will enable a more reliable inference of migration histories and their posterior probabilities, which is required to assess the relative preponderance of seeding of new metastasis by clones from primary tumors and/or existing metastases. Availability and implementation PathFinder is available on the web at https://github.com/SayakaMiura/PathFinder.

HISTORICAL ESSAY: A History of HIV Discovery

Science ◽  
2002 ◽  
Vol 298 (5599) ◽  
pp. 1727-1728 ◽  
Author(s):  
L. Montagnier
Keyword(s):  
Historical Essay ◽  
History Of

The world’s repository at 75: a history of the United Nations Archives*

Comma ◽  
2021 ◽  
Vol 2019 (2) ◽  
pp. 19-36
Author(s):  
Aleksandr Gelfand
Keyword(s):  
United Nations ◽  
San Francisco ◽  
International Organization ◽  
Records Management ◽  
Significant Events ◽  
The World ◽  
History Of ◽  
The United Nations ◽  
Administrative Structures

Seventy-five years ago (1945), the United Nations (UN) was founded in San Francisco by 50 nations. There, a small archives unit served to assemble the first records of the organization; this was the first iteration of today’s Archives and Records Management Section (ARMS). Throughout its history, the fortunes of the UN Archives have waxed and waned, while its role has continuously evolved. Trying to carve out a place for itself within the largest international organization in the world, its physical and administrative structures have undergone profound changes, as has its mission, number of staff, the type of records it holds and its users. This paper examines significant events in the development of the UN Archives, the challenges it has faced and what may be learned from them.

scholarly journals Exploring and Reconstructing Ancestral Anatomies using Ontology-Informed Approaches

2019 ◽  
Vol 3 ◽  
Author(s):  
Sergei Tarasov ◽  
Istvan Miko ◽  
Matthew Yoder ◽  
Josef Uyeda
Keyword(s):  
Phylogenetic Trees ◽  
Character State ◽  
Ancestral Reconstruction ◽  
Anatomy Ontology ◽  
Insect Order ◽  
Ancestral Character State ◽  
Body Regions ◽  
Individual Traits ◽  
History Of ◽  
Complex Characters

Ancestral character state reconstruction has been long used to gain insight into the evolution of individual traits in organisms. However, organismal anatomies (= entire phenotypes) are not merely ensembles of individual traits, rather they are complex systems where traits interact with each other due to anatomical dependencies (when one trait depends on the presence of another trait) and developmental constraints. Comparative phylogenetics has been largely lacking a method for reconstructing the evolution of entire organismal anatomies or organismal body regions. Herein, we present a new approach named PARAMO (Phylogenetic Ancestral Reconstruction of Anatomy by Mapping Ontologies, Tarasov and Uyeda 2019) that takes into account anatomical dependencies and uses stochastic maps (i.e., phylogenetic trees with an instance of mapped evolutionary history of characters, Huelsenbeck et al. 2003) along with anatomy ontologies to reconstruct organismal anatomies. Our approach treats the entire phenotype or its component body regions as single complex characters and allows exploring and comparing phenotypic evolution at different levels of anatomical hierarchy. These complex characters are constructed by ontology-informed amalgamation of elementary characters (i.e., those coded in character matrix) using stochastic maps. In our approach, characters are linked with the terms from an anatomy ontology, which allows viewing them not just as an ensemble of character state tokens but as entities that have their own biological meaning provided by the ontology. This ontology-informed framework provides new opportunities for tracking phenotypic radiations and anatomical evolution of organisms, which we explore using a large dataset for the insect order Hymenoptera (sawflies, wasps, ants and bees).

scholarly journals Agrarian policy of the Ukrainian State on the journals of the meetings of the Council of Ministers

2017 ◽  
Vol 25 (1) ◽  
pp. 189
Author(s):  
Dmytro Volodymyrovych Arkhireyskyi
Keyword(s):  
Information Content ◽  
Land Reform ◽  
Price Policy ◽  
Land Ownership ◽  
Agrarian Policy ◽  
Policy Information ◽  
History Of ◽  
Military Command ◽  
Council Of Ministers

The information content of the journals (minutes) of the meetings of the Council of Ministers of the Ukrainian State (1918) is investigated, which makes it possible to clarify the specifics of governmental agrarian policy. Information on the influence of the German and Austro-Hungarian military command on the agrarian policy of Ukraine, the peculiarities of land ownership and agrarian relations, the food and price policy of the Ukrainian government, and attempts at agrarian and land reform are discussed. The journals of the meetings of the Council of Ministers contain information about the emergence of a peasant rebel movement, caused in general by the unsuccessful agrarian activity of Hetman P. Skoropadsky, and also about government measures aimed at suppressing this movement. The investigated documentary complex should be recognized as an important source on the history of not only the Ukrainian State, its agrarian policy, but also the insurrectional movement and the Ukrainian Revolution of 1917−1921 generally.

scholarly journals Correspondence of S.F. Platonov and M.M. Bogoslovsky

2021 ◽  
pp. 174-184
Author(s):  
Andrey V. Melnikov ◽  
Keyword(s):  
Social Life ◽  
Educational Institutions ◽  
Historical Science ◽  
The Public ◽  
Significant Events ◽  
The Everyday ◽  
Science In Russia ◽  
Public Consciousness ◽  
History Of ◽  
Academy Of Sciences

The article is devoted to the source features of a unique documentary complex – the correspondence of two major Russian historians S.F. Platonov (1860–1933) and M.M. Bogoslovsky (1867–1929). The epistolary dialogue of scientists is of considerable interest not only in terms of studying their life and work. The confidential correspondence reflects significant events in the scientific and social life of Russia, Moscow, Petersburg-Petrograd-Leningrad. Correspondence is a valuable historical and historiographic source not only for understanding the development of historical science in Russia, the formation of Moscow and St. Petersburg historical schools, but also for studying the public consciousness of the Russian humanitarian intelligentsia at the end of the 19th — first third of the 20th centuries, in-depth knowledge of the culture of a turning point in the history of Russia. The letters contain valuable information about the everyday life and life of the professors, the organization of scientific life at the Academy of Sciences, the Archaeographic commission, at Moscow university and the Moscow theological academy, at the Moscow higher courses for women, at the Institute of history of the RANION, the Historical Museum, other higher educational institutions and scientific societies two capitals, they reflect the international ties of domestic historical science with scientists from Great Britain, Germany, France, USA, Czech Republic.

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