scholarly journals Codon evolution: Mechanisms and Models

2012 ◽  
Vol 4 (1) ◽  
pp. 8 ◽  
Author(s):  
Stinus Lindgreen
Keyword(s):  
Codon Evolution

scholarly journals Features of Recent Codon Evolution: A Comparative Polymorphism-Fixation Study

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Zhongming Zhao ◽  
Cizhong Jiang
Keyword(s):  
Amino Acid ◽  
Protein Evolution ◽  
Purifying Selection ◽  
Nucleotide Polymorphism ◽  
Strong Difference ◽  
Codon Composition ◽  
Mutational Pattern ◽  
Codon Positions ◽  
Polymorphism Level ◽  
Codon Evolution

Features of amino-acid and codon changes can provide us important insights on protein evolution. So far, investigators have often examined mutation patterns at either interspecies fixed substitution or intraspecies nucleotide polymorphism level, but not both. Here, we performed a unique analysis of a combined set of intra-species polymorphisms and inter-species substitutions in human codons. Strong difference in mutational pattern was found at codon positions 1, 2, and 3 between the polymorphism and fixation data. Fixation had strong bias towards increasing the rarest codons but decreasing the most frequently used codons, suggesting that codon equilibrium has not been reached yet. We detected strong CpG effect on CG-containing codons and subsequent suppression by fixation. Finally, we detected the signature of purifying selection against A∣U dinucleotides at synonymous dicodon boundaries. Overall, fixation process could effectively and quickly correct the volatile changes introduced by polymorphisms so that codon changes could be gradual and directional and that codon composition could be kept relatively stable during evolution.

LOW RATES OF BINDIN CODON EVOLUTION IN LECITHOTROPHIC HELIOCIDARIS SEA URCHINS

Evolution ◽  
2012 ◽  
Vol 66 (6) ◽  
pp. 1709-1721 ◽  
Author(s):  
Michael W. Hart ◽  
Iva Popovic ◽  
Richard B. Emlet
Keyword(s):  
Sea Urchins ◽  
Codon Evolution

Codon evolution is governed by linear formulas

Amino Acids ◽  
2008 ◽  
Vol 34 (4) ◽  
pp. 661-668 ◽  
Author(s):  
K. Sorimachi ◽  
T. Okayasu
Keyword(s):  
Codon Evolution

scholarly journals On the interpretation of results returned by branch-site models

2015 ◽  
Author(s):  
Stephane Guindon
Keyword(s):  
Positive Selection ◽  
Negative Selection ◽  
Molecular Level ◽  
Site Model ◽  
Branch Site ◽  
Codon Evolution ◽  
Interpretation Of Results

In a recent study, Murrell et al. (2015) compared the performance of several branch-site models of codon evolution. Their interpretation of results published by Lu & Guindon (2014) suggests that the stochastic branch-site model implemented in the software fitmodel is anti-conservative altogether, i.e., positive selection is detected more often than expected when analyzing sequences evolving under a mixture of neutrality and negative selection. I argue here that this presentation of the performance of fitmodel is misleading and should not deter evolutionary biologists from using this approach in exploratory analyses of selection patterns at the molecular level.

scholarly journals Unbiased estimate of synonymous and non-synonymous substitution rates with non-stationary base composition

2017 ◽  
Author(s):  
Laurent Guéguen ◽  
Laurent Duret
Keyword(s):  
Base Composition ◽  
Evolutionary Process ◽  
Synonymous Substitution ◽  
Substitution Rates ◽  
Synonymous Mutations ◽  
Synonymous Substitution Rates ◽  
Good Proxy ◽  
Neutral Mutations ◽  
Stochastic Mapping ◽  
Codon Evolution

AbstractThe measure of synonymous and non-synonymous substitution rates (dS and dN) is useful for assessing selection operating on protein sequences or for investigating mutational processes affecting genomes. In particular, the ratio is expected to be a good proxy of ω, the probability of fixation of non-synonymous mutations relative to that of neutral mutations. Standard methods for estimating dN, dS or ω rely on the assumption that the base composition of sequences is at the equilibrium of the evolutionary process. In many clades, this assumption of stationarity is in fact incorrect, and we show here through simulations and through analyses of empirical data that non-stationarity biases the estimate of dN, dS and ω. We show that the bias in the estimate of ω can be fixed by explicitly considering non-stationarity in the modeling of codon evolution, in a maximum likelihood framework. Moreover, we propose an exact method of estimate of dN and dS on branches, based on stochastic mapping, that can take into account non-stationarity. This method can be directly applied to any kind of model of evolution of codons, as long as neutrality is clearly parameterized.

scholarly journals Shedding light on the underlying characteristics of genomes using Kronecker model families of codon evolution

2020 ◽  
Author(s):  
Maryam Zaheri ◽  
Nicolas Salamin
Keyword(s):  
Transition Rate ◽  
Accurate Estimation ◽  
Mechanistic Models ◽  
Rate Matrix ◽  
Nucleotide Level ◽  
Codon Models ◽  
Biological Dataset ◽  
Transition Rate Matrix ◽  
Simplifying Assumptions ◽  
Codon Evolution

AbstractThe mechanistic models of codon evolution rely on some simplistic assumptions in order to reduce the computational complexity of estimating the high number of parameters of the models. This paper is an attempt to investigate how much these simplistic assumptions are misleading when they violate the nature of the biological dataset in hand. We particularly focus on three simplistic assumptions made by most of the current mechanistic codon models including: 1) only single substitutions between nucleotides within codons in the codon transition rate matrix are allowed. 2) mutation is homogenous across nucleotides within a codon. 3) assuming HKY nucleotide model is good enough at the nucleotide level. For this purpose, we developed a framework of mechanistic codon models, each model in the framework hold or relax some of the mentioned simplifying assumptions. Holding or relaxing the three simplistic assumptions results in total to eight different mechanistic models in the framework. Through several experiments on biological datasets and simulations we show that the three simplistic assumptions are unrealistic for most of the biological datasets and relaxing these assumptions lead to accurate estimation of evolutionary parameters such as selection pressure.

scholarly journals Structure of the Glucanase Inhibitor Protein (GIP) Family from Phytophthora Species Suggests Coevolution with Plant Endo-β-1,3-Glucanases

2008 ◽  
Vol 21 (6) ◽  
pp. 820-830 ◽  
Author(s):  
Cynthia M. B. Damasceno ◽  
John G. Bishop ◽  
Daniel R. Ripoll ◽  
Joe Win ◽  
Sophien Kamoun ◽  
...  
Keyword(s):  
Serine Proteases ◽  
Evolutionary Relationship ◽  
Catalytic Triad ◽  
Phytophthora Species ◽  
Arms Race ◽  
Inhibitor Protein ◽  
In Planta ◽  
Temporal Expression ◽  
Close Proximity ◽  
Codon Evolution

During invasion of their plant hosts, species of the oomycete genus Phytophthora secrete glucanase inhibitor proteins (GIPs) into the plant apoplast, which bind and inhibit the activity of plant extracellular endo-β-1,3-glucanases (EGases). GIPs show structural homology to the chymotrypsin class of serine proteases (SP) but lack proteolytic activity due to the absence of an intact catalytic triad and, thus, belong to a broader class of proteins called serine protease homologs (SPH). To study the evolutionary relationship between GIPs and functional SP, database searches were used to identify 48 GIP homologs in the P. sojae, P. ramorum, and P. infestans genomes, composing GIPs, SPH, and potentially functional SP. Analyses of P. infestans–inoculated tomato leaves showed that P. infestans GIPs and tomato EGases are present in the apoplast and form stable complexes in planta. Studies of the temporal expression of a four-membered GIP family from P. infestans (PiGIP1 to PiGIP4) further revealed that the genes show distinctly different patterns during an infection timecourse. Codon evolution analyses of GIP homologs identified several positively selected peptide sites and structural modeling revealed them to be in close proximity to rapidly evolving EGase residues, suggesting that the interaction between GIPs and EGases has the hallmarks of a coevolving molecular arms race.

scholarly journals Phylogenetic Patterns of Codon Evolution in the ACTIN-DEPOLYMERIZING FACTOR/COFILIN (ADF/CFL) Gene Family

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0145917 ◽  
Author(s):  
Eileen M. Roy-Zokan ◽  
Kelly A. Dyer ◽  
Richard B. Meagher
Keyword(s):  
Gene Family ◽  
Actin Depolymerizing Factor ◽  
Codon Evolution
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