scholarly journals Automated selection of homologs to track the evolutionary history of proteins

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Pablo Mier ◽  
Antonio J. Pérez-Pulido ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Evolutionary History ◽  
History Of ◽  
Selection Of

scholarly journals The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1032 ◽  
Author(s):  
Yulia Vakulenko ◽  
Andrei Deviatkin ◽  
Alexander Lukashev
Keyword(s):  
Evolutionary History ◽  
Large Datasets ◽  
Sequencing Errors ◽  
Sample Bias ◽  
Phylogenetic Studies ◽  
Phylogenetic Methods ◽  
History Of ◽  
Sequence Position ◽  
Annotation Errors ◽  
Selection Of

Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well-described in the literature. The preparation of a sequence dataset is less formalized, but its impact can be even more profound. This article used simulated datasets of enterovirus sequences to evaluate the effect of sample bias on picornavirus phylogenetic studies. Possible approaches to the reduction of large datasets and their potential for introducing additional artefacts were demonstrated. The most consistent results were obtained using “smart sampling”, which reduced sequence subsets from large studies more than those from smaller ones in order to preserve the rare sequences in a dataset. The effect of sequences with technical or annotation errors in the Bayesian framework was also analyzed. Sequences with about 0.5% sequencing errors or incorrect isolation dates altered by just 5 years could be detected by various approaches, but the efficiency of identification depended upon sequence position in a phylogenetic tree. Even a single erroneous sequence could profoundly destabilize the whole analysis by increasing the variance of the inferred evolutionary parameters.

Mosaic evolution in the middle Miocene planktonic foraminifera Fohsella lineage

Paleobiology ◽  
2018 ◽  
Vol 44 (2) ◽  
pp. 263-272
Author(s):  
Weimin Si ◽  
William A. Berggren ◽  
Marie-Pierre Aubry
Keyword(s):  
Evolutionary History ◽  
Middle Miocene ◽  
Planktonic Foraminifera ◽  
Phenotypic Traits ◽  
Geographic Ranges ◽  
History Of ◽  
Morphologic Evolution ◽  
Coiling Direction ◽  
Directional Trend ◽  
Selection Of

AbstractRecent studies have shown that modes of evolution, namely directional trend, random walk, and stasis, vary across morphologic traits and over the geographic range of a taxon. If so, is it possible that our interpretation of evolutionary modes is actually driven by our selection of traits in a study? In an attempt to answer this question, we have restudied the middle Miocene planktonic foraminifera Fohsella lineage, an iconic example of gradual morphologic evolution. In contrast to previous studies that have focused on the gross morphology as embodied by the edge view of tests, we analyze here multiple phenotypic traits chosen because their biologic and ecologic significance is well understood in living populations. We find that traits in the lineage did not evolve in concert. The timing and geographic pattern of changes in shape, coiling direction, size, and ecology were different. The evolution of this lineage is a mosaic combination of different evolutionary modes for different traits. We suggest that overemphasis on the evolution of some single trait, such as the edge-view outline, from narrow geographic ranges has significantly underestimated the dynamic evolutionary history of this group.

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
Kevin Arceneaux
Keyword(s):  
Decision Making ◽  
Individual Differences ◽  
Cognitive Processes ◽  
Evolutionary History ◽  
Behavioral Responses ◽  
History Of ◽  
Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

Conclusion: What is Speculative Empiricism?

2018 ◽  
Author(s):  
Didier Debaise
Keyword(s):  
Social Groups ◽  
Speculative Philosophy ◽  
System P ◽  
History Of ◽  
Selection Of

Process and Reality ends with a warning: ‘[t]he chief danger to philosophy is narrowness in the selection of evidence’ (PR, 337). Although this danger of narrowness might emerge from the ‘idiosyncrasies and timidities of particular authors, of particular social groups, of particular schools of thought, of particular epochs in the history of civilization’ (PR, 337), we should not be mistaken: it occurs within philosophy, in its activity, its method. And the fact that this issue arises at the end of Process and Reality reveals the ambition that has accompanied its composition: Whitehead has resisted this danger through the form and ambition of his speculative construction. The temptation of a narrowness in selection attempts to expel speculative philosophy at the same time as it haunts each part of its system.

Displace of Documentary Heritage from the Soviet Union to Poland during the Third Decade of the XXth Century

2014 ◽  
Vol 3 ◽  
pp. 127-137
Author(s):  
Tatsiana Hiarnovich
Keyword(s):  
Soviet Union ◽  
International Agreements ◽  
Peace Treaty ◽  
Actual Process ◽  
Xxth Century ◽  
The Third ◽  
The Soviet Union ◽  
History Of ◽  
Selection Of

The paper explores the displace of Polish archives from the Soviet Union that was performed in 1920s according to the Riga Peace Treaty of 1921 and other international agreements. The aim of the research is to reconstruct the process of displace, based on the archival sources and literature. The object of the research is those documents that were preserved in the archives of Belarus and together with archives from other republics were displaced to Poland. The exploration leads to clarification of the selection of document fonds to be displaced, the actual process of movement and the explanation of the role that the archivists of Belarus performed in the history of cultural relationships between Poland and the Soviet Union. The articles of the Treaty of Riga had been formulated without taking into account the indivisibility of archive fonds that is one of the most important principles of restitution, which caused the failure of the treaty by the Soviet part.

Diagnostic approach to causes of spinal pain

2018 ◽  
pp. 66-70
Author(s):  
F. D. Nasirova
Keyword(s):  
Spinal Pain ◽  
Rapid Loss ◽  
Loss Of Weight ◽  
History Of ◽  
Radiologic Investigation ◽  
Males And Females ◽  
Serious Disease ◽  
Pain At Rest ◽  
Oncologic Diseases ◽  
Selection Of

Causes of spinal pain are extremely varying. Sex composition of patients referring with spinal pain at the age of 16 to 35 was 35% and 65% for males and females, respectively. Peak number of complaints was observed in 30-40 years age group of highest work ability. The followings should be considered as precautions in spinal pain: onset of pain at the age of 20 and after 50, family history of oncologic diseases, walking disorders or dysfunctions of sphincters, numbness in extremities, general malaise and rapid loss of weight, pain at rest and primarily at night, as these conditions may be a warning of underlying serious disease. Selection of algorithm for radiologic investigation is decided by the treating physician.

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