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Shin-han Shiu - One of the best experts on this subject based on the ideXlab platform.
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the nonsynonymous synonymous Substitution Rate ratio versus the radical conservative replacement Rate ratio in the evolution of mammalian genes
Molecular Biology and Evolution, 2007Co-Authors: Kousuke Hanada, Shin-han ShiuAbstract:There are 2 ways to infer selection pressures in the evolution of protein-coding genes, the nonsynonymous and synonymous Substitution Rate ratio (K(A)/K(S)) and the radical and conservative amino acid replacement Rate ratio (K(R)/K(C)). Because the K(R)/K(C) ratio depends on the definition of radical and conservative changes in the classification of amino acids, we develop an amino acid classification that maximizes the correlation between K(A)/K(S) and K(R)/K(C). An analysis of 3,375 orthologous gene groups among 5 mammalian species shows that our classification gives a significantly higher correlation coefficient between the 2 ratios than those of existing classifications. However, there are many orthologous gene groups with a low K(A)/K(S) but a high K(R)/K(C) ratio. Examining the functions of these genes, we found an overrepresentation of functional categories related to development. To determine if the overrepresentation is stage specific, we examined the expression patterns of these genes at different developmental stages of the mouse. Interestingly, these genes are highly expressed in the early middle stage of development (blastocyst to amnion). It is commonly thought that developmental genes tend to be conservative in evolution, but some molecular changes in developmental stages should have contributed to morphological divergence in adult mammals. Therefore, we propose that the relaxed pressures indicated by the K(R)/K(C) ratio but not by K(A)/K(S) in the early middle stage of development may be important for the morphological divergence of mammals at the adult stage, whereas purifying selection detected by K(A)/K(S) occurs in the early middle developmental stage.
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The Nonsynonymous/Synonymous Substitution Rate Ratio versus the Radical/Conservative Replacement Rate Ratio in the Evolution of Mammalian Genes
Molecular biology and evolution, 2007Co-Authors: Kousuke Hanada, Shin-han ShiuAbstract:There are 2 ways to infer selection pressures in the evolution of protein-coding genes, the nonsynonymous and synonymous Substitution Rate ratio (K(A)/K(S)) and the radical and conservative amino acid replacement Rate ratio (K(R)/K(C)). Because the K(R)/K(C) ratio depends on the definition of radical and conservative changes in the classification of amino acids, we develop an amino acid classification that maximizes the correlation between K(A)/K(S) and K(R)/K(C). An analysis of 3,375 orthologous gene groups among 5 mammalian species shows that our classification gives a significantly higher correlation coefficient between the 2 ratios than those of existing classifications. However, there are many orthologous gene groups with a low K(A)/K(S) but a high K(R)/K(C) ratio. Examining the functions of these genes, we found an overrepresentation of functional categories related to development. To determine if the overrepresentation is stage specific, we examined the expression patterns of these genes at different developmental stages of the mouse. Interestingly, these genes are highly expressed in the early middle stage of development (blastocyst to amnion). It is commonly thought that developmental genes tend to be conservative in evolution, but some molecular changes in developmental stages should have contributed to morphological divergence in adult mammals. Therefore, we propose that the relaxed pressures indicated by the K(R)/K(C) ratio but not by K(A)/K(S) in the early middle stage of development may be important for the morphological divergence of mammals at the adult stage, whereas purifying selection detected by K(A)/K(S) occurs in the early middle developmental stage.
Kousuke Hanada - One of the best experts on this subject based on the ideXlab platform.
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the nonsynonymous synonymous Substitution Rate ratio versus the radical conservative replacement Rate ratio in the evolution of mammalian genes
Molecular Biology and Evolution, 2007Co-Authors: Kousuke Hanada, Shin-han ShiuAbstract:There are 2 ways to infer selection pressures in the evolution of protein-coding genes, the nonsynonymous and synonymous Substitution Rate ratio (K(A)/K(S)) and the radical and conservative amino acid replacement Rate ratio (K(R)/K(C)). Because the K(R)/K(C) ratio depends on the definition of radical and conservative changes in the classification of amino acids, we develop an amino acid classification that maximizes the correlation between K(A)/K(S) and K(R)/K(C). An analysis of 3,375 orthologous gene groups among 5 mammalian species shows that our classification gives a significantly higher correlation coefficient between the 2 ratios than those of existing classifications. However, there are many orthologous gene groups with a low K(A)/K(S) but a high K(R)/K(C) ratio. Examining the functions of these genes, we found an overrepresentation of functional categories related to development. To determine if the overrepresentation is stage specific, we examined the expression patterns of these genes at different developmental stages of the mouse. Interestingly, these genes are highly expressed in the early middle stage of development (blastocyst to amnion). It is commonly thought that developmental genes tend to be conservative in evolution, but some molecular changes in developmental stages should have contributed to morphological divergence in adult mammals. Therefore, we propose that the relaxed pressures indicated by the K(R)/K(C) ratio but not by K(A)/K(S) in the early middle stage of development may be important for the morphological divergence of mammals at the adult stage, whereas purifying selection detected by K(A)/K(S) occurs in the early middle developmental stage.
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The Nonsynonymous/Synonymous Substitution Rate Ratio versus the Radical/Conservative Replacement Rate Ratio in the Evolution of Mammalian Genes
Molecular biology and evolution, 2007Co-Authors: Kousuke Hanada, Shin-han ShiuAbstract:There are 2 ways to infer selection pressures in the evolution of protein-coding genes, the nonsynonymous and synonymous Substitution Rate ratio (K(A)/K(S)) and the radical and conservative amino acid replacement Rate ratio (K(R)/K(C)). Because the K(R)/K(C) ratio depends on the definition of radical and conservative changes in the classification of amino acids, we develop an amino acid classification that maximizes the correlation between K(A)/K(S) and K(R)/K(C). An analysis of 3,375 orthologous gene groups among 5 mammalian species shows that our classification gives a significantly higher correlation coefficient between the 2 ratios than those of existing classifications. However, there are many orthologous gene groups with a low K(A)/K(S) but a high K(R)/K(C) ratio. Examining the functions of these genes, we found an overrepresentation of functional categories related to development. To determine if the overrepresentation is stage specific, we examined the expression patterns of these genes at different developmental stages of the mouse. Interestingly, these genes are highly expressed in the early middle stage of development (blastocyst to amnion). It is commonly thought that developmental genes tend to be conservative in evolution, but some molecular changes in developmental stages should have contributed to morphological divergence in adult mammals. Therefore, we propose that the relaxed pressures indicated by the K(R)/K(C) ratio but not by K(A)/K(S) in the early middle stage of development may be important for the morphological divergence of mammals at the adult stage, whereas purifying selection detected by K(A)/K(S) occurs in the early middle developmental stage.
R. De Wachter - One of the best experts on this subject based on the ideXlab platform.
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construction of evolutionary distance trees with treecon for windows accounting for variation in nucleotide Substitution Rate among sites
Bioinformatics, 1997Co-Authors: Yves Van De Peer, R. De WachterAbstract:Motivation: To improve the estimation of evolutionary distances between nucieotide sequences by considering the differences in Substitution Rates among sites. Results: TREECON for Windows (Van de Peer.Y. and De Wachter.R. Comput. Applic. Biosci., 9, 569-570, 1994) is a software package for the construction and drawing of phylogenetic trees based on distance data computed from nucleic acid and amino acid sequences. For nucleic acids, we here describe the implementation of a recently developed method for estimating evolutionary distances taking into account the Substitution Rate of individual sites in a sequence alignment. Availability: TREECON for Windows is available on request from the authors. A small fee is asked in order to support the work and to reinvest in new computer hard- and software. More information about the program and Substitution Rate calibration can be found at URL http://bioc-www.uia.ac.be/uJ yvdp/treeconw. html. Contact: E-mail: yvdp@uia.ua.ac.be
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Substitution Rate calibration of small subunit ribosomal rna identifies chlorarachniophyte endosymbionts as remnants of green algae
Proceedings of the National Academy of Sciences of the United States of America, 1996Co-Authors: Yves Van De Peer, Uwe G. Maier, Stefan A Rensing, R. De WachterAbstract:Abstract Chlorarachniophytes are amoeboid algae with chlorophyll a and b containing plastids that are surrounded by four membranes instead of two as in plants and green algae. These extra membranes form important support for the hypothesis that chlorarachniophytes have acquired their plastids by the ingestion of another eukaryotic plastid-containing alga. Chlorarachniophytes also contain a small nucleus-like structure called the nucleomorph situated between the two inner and the two outer membranes surrounding the plastid. This nucleomorph is a remnant of the endosymbiont's nucleus and encodes, among other molecules, small subunit ribosomal RNA. Previous phylogenetic analyses on the basis of this molecule provided unexpected and contradictory evidence for the origin of the chlorarachniophyte endosymbiont. We developed a new method for measuring the Substitution Rates of the individual nucleotides of small subunit ribosomal RNA. From the resulting Substitution Rate distribution, we derived an equation that gives a more realistic relationship between sequence dissimilarity and evolutionary distance than equations previously available. Phylogenetic trees constructed on the basis of evolutionary distances computed by this new method clearly situate the chlorarachniophyte nucleomorphs among the green algae. Moreover, this relationship is confirmed by transversion analysis of the Chlorarachnion plastid small subunit ribosomal RNA.
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the evolution of stramenopiles and alveolates as derived by Substitution Rate calibration of small ribosomal subunit rna
Journal of Molecular Evolution, 1996Co-Authors: Yves Van De Peer, Gert Van Der Auwera, R. De WachterAbstract:The Substitution Rate of the individual positions in an alignment of 750 eukaryotic small ribosomal subunit RNA sequences was estimated. From the resulting Rate distribution, an equation was derived that gives a more precise relationship between sequence dissimilarity and evolutionary distance than hitherto available. Trees constructed on the basis of evolutionary distances computed by this new equation for small ribosomal subunit RNA sequences from ciliates, apicomplexans, dinoflagellates, oomycetes, hyphochytriomycetes, bicosoecids, labyrinthuloids, and heterokont algae show a more consistent tree topology than trees constructed in the absence of “Substitution Rate calibration.” In particular, they do not suffer from anomalies caused by the presence of extremely long branches.
Michael Bulmer - One of the best experts on this subject based on the ideXlab platform.
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Synonymous Substitution Rates in enterobacteria.
Genetics, 1995Co-Authors: Adam Eyre-walker, Michael BulmerAbstract:It has been shown previously that the synonymous Substitution Rate between Escherichia coli and Salmonella typhimurium is lower in highly than in weakly expressed genes, and it has been suggested that this is due to stronger selection for translational efficiency in highly expressed genes as reflected in their greater codon usage bias. This hypothesis is tested here by comparing the Substitution Rate in codon families with different patterns of synonymous codon use. It is shown that the decline in the Substitution Rate across expression levels is as great for codon families that do not appear to be subject to selection for translational efficiency as for those that are. This implies that selection on translational efficiency is not responsible for the decline in the Substitution Rate across genes. It is argued that the most likely explanation for this decline is a decrease in the mutation Rate. It is also shown that a simple evolutionary model in which synonymous codon use is determined by a balance between mutation, selection for an optimal codon, and genetic drift predicts that selection should have little effect on the Substitution Rate in the present case.
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Reduced synonymous Substitution Rate at the start of enterobacterial genes.
Nucleic acids research, 1993Co-Authors: Adam Eyre-walker, Michael BulmerAbstract:It has been shown previously that the synonymous Substitution Rate between Escherichia coli and Salmonella typhimurium is lower in highly than in weakly expressed genes, and it has been suggested that this is due to stronger selection for translational efficiency in highly expressed genes as reflected in their greater codon usage bias. This hypothesis is tested here by comparing the Substitution Rate in codon families with different patterns of synonymous codon use. It is shown that the decline in the Substitution Rate across expression levels is as great for codon families that do not appear to be subject to selection for translational efficiency as for those that are. This implies that selection on translational efficiency is not responsible for the decline in the Substitution Rate across genes. It is argued that the most likely explanation for this decline is a decrease in the mutation Rate. It is also shown that a simple evolutionary model in which synonymous codon use is determined by a balance between mutation, selection for an optimal codon, and genetic drift predicts that selection should have little effect on the Substitution Rate in the present case.
Nicolas Galtier - One of the best experts on this subject based on the ideXlab platform.
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is adaptation limited by mutation a timescale dependent effect of genetic diversity on the adaptive Substitution Rate in animals
PLOS Genetics, 2020Co-Authors: Marjolaine Rousselle, Paul Simion, Marieka Tilak, Emeric Figuet, Benoit Nabholz, Nicolas GaltierAbstract:Whether adaptation is limited by the beneficial mutation supply is a long-standing question of evolutionary genetics, which is more generally related to the determination of the adaptive Substitution Rate and its relationship with species effective population size (Ne) and genetic diversity. Empirical evidence reported so far is equivocal, with some but not all studies supporting a higher adaptive Substitution Rate in large-Ne than in small-Ne species. We gathered coding sequence polymorphism data and estimated the adaptive amino-acid Substitution Rate ωa, in 50 species from ten distant groups of animals with markedly different population mutation Rate θ. We reveal the existence of a complex, timescale dependent relationship between species adaptive Substitution Rate and genetic diversity. We find a positive relationship between ωa and θ among closely related species, indicating that adaptation is indeed limited by the mutation supply, but this was only true in relatively low-θ taxa. In contrast, we uncover no significant correlation between ωa and θ at a larger taxonomic scale, suggesting that the proportion of beneficial mutations scales negatively with species' long-term Ne.
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is adaptation limited by mutation a timescale dependent effect of genetic diversity on the adaptive Substitution Rate in animals
bioRxiv, 2019Co-Authors: Marjolaine Rousselle, Paul Simion, Marieka Tilak, Emeric Figuet, Benoit Nabholz, Nicolas GaltierAbstract:ABSTRACT Whether adaptation is limited by the beneficial mutation supply is a long-standing question of evolutionary genetics, which is more generally related to the determination of the adaptive Substitution Rate and its relationship with the effective population size Ne. Empirical evidence reported so far is equivocal, with some but not all studies supporting a higher adaptive Substitution Rate in large-Ne than in small-Ne species. We gathered coding sequence polymorphism data and estimated the adaptive amino-acid Substitution Rate ωa, in 50 species from ten distant groups of animals with markedly different population mutation Rate θ. We reveal the existence of a complex, timescale dependent relationship between species adaptive Substitution Rate and genetic diversity. We find a positive relationship between ωa and θ among closely related species, indicating that adaptation is indeed limited by the mutation supply, but this was only true in relatively low-θ taxa. In contrast, we uncover a weak negative correlation between ωa and θ at a larger taxonomic scale. This result is consistent with Fisher’s geometrical model predictions and suggests that the proportion of beneficial mutations scales negatively with species’ long-term Ne.
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overestimation of the adaptive Substitution Rate in fluctuating populations
Biology Letters, 2018Co-Authors: Marjolaine Rousselle, Benoit Nabholz, Maeva Mollion, Thomas Bataillon, Nicolas GaltierAbstract:Estimating the proportion of adaptive Substitutions ( α ) is of primary importance to uncover the determinants of adaptation in comparative genomic studies. Several methods have been proposed to estimate α from patterns polymorphism and divergence in coding sequences. However, estimators of α can be biased when the underlying assumptions are not met. Here we focus on a potential source of bias, i.e. variation through time in the long-term population size ( N ) of the considered species. We show via simulations that ancient demographic fluctuations can geneRate severe overestimations of α , and this is irrespective of the recent population history.
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Extreme Variation of mtDNA Neutral Substitution Rate across Mammalian Species - the Longevity Hypothesis
Molecular Biology and Evolution, 2008Co-Authors: Benoit Nabholz, Sylvain Glémin, Nicolas GaltierAbstract:Numerical values in the last paragraph of the Results section (p.124) are false. The paragraph should read : ‘‘Mitochondrial lineage-specific Substitution Rates were estimated from amino-acid sequences for comparative purposes. Non-synonymous and third codon position Substitution Rates were well correlated (R 5 0.442, p-val , 0.0001). The median estimated Rate was 0.002 amino-acid Substitution per site per million year. The Rodentia average was 0.0044 i.e. ;10 times faster than in Lagomorpha (0.0004). This shows that non-synonymous Substitution Rates are less variable between mammalian lineages than synonymous Substitution Rates.’’
