Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs

2018 ◽  
pp. 187-195 ◽  
Author(s):  
Aysan Ghasemzadeh ◽  
Marta Małgorzata ter Haar ◽  
Masoud Shams-bakhsh ◽  
Walter Pirovano ◽  
Vitantonio Pantaleo
Keyword(s):  
Shannon Entropy ◽  
Substitution Rate ◽  
Rate Variation ◽  
Substitution Rate Variation

scholarly journals Erratum to: Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs

2018 ◽  
pp. E1-E1
Author(s):  
Aysan Ghasemzadeh ◽  
Marta Małgorzata ter Haar ◽  
Masoud Shams-bakhsh ◽  
Walter Pirovano ◽  
Vitantonio Pantaleo
Keyword(s):  
Shannon Entropy ◽  
Substitution Rate ◽  
Rate Variation ◽  
Substitution Rate Variation

Viral Substitution Rate Variation Can Arise from the Interplay between Within-Host and Epidemiological Dynamics

2013 ◽  
Vol 182 (4) ◽  
pp. 494-513 ◽  
Author(s):  
Stacy O. Scholle ◽  
Rolf J. F. Ypma ◽  
Alun L. Lloyd ◽  
Katia Koelle
Keyword(s):  
Substitution Rate ◽  
Rate Variation ◽  
Substitution Rate Variation

scholarly journals Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae

2009 ◽  
Vol 9 (1) ◽  
pp. 260 ◽  
Author(s):  
Daniel B Sloan ◽  
Bengt Oxelman ◽  
Anja Rautenberg ◽  
Douglas R Taylor
Keyword(s):  
Phylogenetic Analysis ◽  
Substitution Rate ◽  
Rate Variation ◽  
Substitution Rate Variation

scholarly journals Compensatory Evolution in RNA Secondary Structures Increases Substitution Rate Variation among Sites

2008 ◽  
Vol 25 (8) ◽  
pp. 1778-1787 ◽  
Author(s):  
J. L. Knies ◽  
K. K. Dang ◽  
T. J. Vision ◽  
N. G. Hoffman ◽  
R. Swanstrom ◽  
...  
Keyword(s):  
Substitution Rate ◽  
Secondary Structures ◽  
Rate Variation ◽  
Rna Secondary Structures ◽  
Compensatory Evolution ◽  
Substitution Rate Variation

scholarly journals An improved method for fitting gamma distribution to substitution rate variation among sites

2018 ◽  
Author(s):  
Xuhua Xia
Keyword(s):  
Gamma Distribution ◽  
Substitution Rate ◽  
Shape Parameter ◽  
Pairwise Comparison ◽  
Simultaneous Estimation ◽  
Rate Variation ◽  
Simple Method ◽  
Site Specific ◽  
Specific Number ◽  
Substitution Rate Variation

AbstractGamma distribution has been used to fit substitution rate variation over site. One simple method to estimate the shape parameter of the gamma distribution is to 1) reconstruct a phylogenetic tree and the ancestral states of internal nodes, 2) perform pairwise comparison between nodes on each side of each branch to count the number of “observed” substitutions for each site, and apply correction of multiple hits to derive the estimated number of substitutions for each site, and 3) fit the site-specific substitution data to gamma distribution to obtain the shape parameter α This method is fast but its accuracy depends much on the accuracy of the estimated site-specific number of substitutions. The existing method has three shortcomings. First, it uses Poisson correction which is inadequate for almost any nucleotide sequences. Second, it does independent estimation for the number of substitutions at each site without making use of information at all sites. Third, the program implementing the method has never been made publically available. I have implemented in DAMBE software a new method based on the F84 substitution model with simultaneous estimation that uses information from all sites in estimating the number of substitutions at each site. DAMBE is freely available at available athttp://dambe.bio.uottawa.ca

scholarly journals Substitution rate variation in closely related rodent species

Heredity ◽  
1997 ◽  
Vol 78 (1) ◽  
pp. 21-31 ◽  
Author(s):  
Dan Fieldhouse ◽  
Fariborz Yazdani ◽  
G Brian Golding
Keyword(s):  
Substitution Rate ◽  
Rodent Species ◽  
Rate Variation ◽  
Substitution Rate Variation

scholarly journals Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril

2020 ◽  
Vol 37 (8) ◽  
pp. 2430-2439 ◽  
Author(s):  
Sadie R Wisotsky ◽  
Sergei L Kosakovsky Pond ◽  
Stephen D Shank ◽  
Spencer V Muse
Keyword(s):  
False Positive ◽  
Substitution Rate ◽  
Simulated Data ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Rate Variation ◽  
Nonsynonymous Substitution Rate ◽  
Selection Testing ◽  
The Impact ◽  
Substitution Rate Variation

Abstract Most molecular evolutionary studies of natural selection maintain the decades-old assumption that synonymous substitution rate variation (SRV) across sites within genes occurs at levels that are either nonexistent or negligible. However, numerous studies challenge this assumption from a biological perspective and show that SRV is comparable in magnitude to that of nonsynonymous substitution rate variation. We evaluated the impact of this assumption on methods for inferring selection at the molecular level by incorporating SRV into an existing method (BUSTED) for detecting signatures of episodic diversifying selection in genes. Using simulated data we found that failing to account for even moderate levels of SRV in selection testing is likely to produce intolerably high false positive rates. To evaluate the effect of the SRV assumption on actual inferences we compared results of tests with and without the assumption in an empirical analysis of over 13,000 Euteleostomi (bony vertebrate) gene alignments from the Selectome database. This exercise reveals that close to 50% of positive results (i.e., evidence for selection) in empirical analyses disappear when SRV is modeled as part of the statistical analysis and are thus candidates for being false positives. The results from this work add to a growing literature establishing that tests of selection are much more sensitive to certain model assumptions than previously believed.

scholarly journals The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis

2019 ◽  
Vol 15 ◽  
pp. 117693431985598 ◽  
Author(s):  
Beatriz Mello ◽  
Carlos G Schrago
Keyword(s):  
Substitution Rate ◽  
Relative Rate ◽  
Gene Tree ◽  
Great Apes ◽  
Rate Variation ◽  
Evolutionary Trend ◽  
Branch Lengths ◽  
Alternative Scenarios ◽  
Genomic Regions ◽  
Substitution Rate Variation

The recent surge of genomic data has prompted the investigation of substitution rate variation across the genome, as well as among lineages. Evolutionary trees inferred from distinct genomic regions may display branch lengths that differ between loci by simple proportionality constants, indicating that rate variation follows a pacemaker model, which may be attributed to lineage effects. Analyses of genes from diverse biological clades produced contrasting results, supporting either this model or alternative scenarios where multiple pacemakers exist. So far, an evaluation of the pacemaker hypothesis for all great apes has never been carried out. In this work, we tested whether the evolutionary rates of hominids conform to pacemakers, which were inferred accounting for gene tree/species tree discordance. For higher precision, substitution rates in branches were estimated with a calibration-free approach, the relative rate framework. A predominant evolutionary trend in great apes was evidenced by the recovery of a large pacemaker, encompassing most hominid genomic regions. In addition, the majority of genes followed a pace of evolution that was closely related to the strict molecular clock. However, slight rate decreases were recovered in the internal branches leading to humans, corroborating the hominoid slowdown hypothesis. Our findings suggest that in great apes, life history traits were the major drivers of substitution rate variation across the genome.

scholarly journals Correlates of substitution rate variation in mammalian protein-coding sequences

2008 ◽  
Vol 8 (1) ◽  
pp. 53 ◽  
Author(s):  
John J Welch ◽  
Olaf RP Bininda-Emonds ◽  
Lindell Bromham
Keyword(s):  
Substitution Rate ◽  
Rate Variation ◽  
Protein Coding ◽  
Coding Sequences ◽  
Substitution Rate Variation ◽  
Mammalian Protein
Sign in / Sign up

Export Citation Format

Share Document