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Journal articles on the topic 'Substitution rate evolution'
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1
Woolfit, Megan. "Effective population size and the rate and pattern of nucleotide substitutions." Biology Letters 5, no. 3 (April 8, 2009): 417–20. http://dx.doi.org/10.1098/rsbl.2009.0155.
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Both the overall rate of nucleotide substitution and the relative proportions of synonymous and non-synonymous substitutions are predicted to vary between species that differ in effective population size ( N e ). Our understanding of the genetic processes underlying these lineage-specific differences in molecular evolution is still developing. Empirical analyses indicate that variation in substitution rates and patterns caused by differences in N e is often substantial, however, and must be accounted for in analyses of molecular evolution.
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Streck, André Felipe, Sandro Luis Bonatto, Timo Homeier, Carine Kunzler Souza, Karla Rathje Gonçalves, Danielle Gava, Cláudio Wageck Canal, and Uwe Truyen. "High rate of viral evolution in the capsid protein of porcine parvovirus." Journal of General Virology 92, no. 11 (November 1, 2011): 2628–36. http://dx.doi.org/10.1099/vir.0.033662-0.
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In recent years, it has been shown that some parvoviruses exhibit high substitution rates, close to those of RNA viruses. In order to monitor and determine new mutations in porcine parvovirus (PPV), recent PPV field isolates from Austria, Brazil, Germany and Switzerland were sequenced and analysed. These samples, together with sequences retrieved from GenBank, were included in three datasets, consisting of the complete NS1 and VP1 genes and a partial VP1 gene. For each dataset, the nucleotide substitution rate and the molecular clock were determined. Analysis of the PPV field isolates revealed that a recently described amino acid substitution, S436T, appeared to be common in the VP2 protein in the Austrian, Brazilian and German virus populations. Furthermore, new amino acid substitutions were identified, located mainly in the viral capsid loops. By inferring the evolutionary dynamics of the PPV sequences, nucleotide substitution rates of approximately 10−5 substitutions per site per year for the non-structural protein gene and 10−4 substitutions per site per year for the capsid protein gene (for both viral protein datasets) were found. The latter rate is similar to those commonly found in RNA viruses. An association of the phylogenetic tree with the molecular clock analysis revealed that the mutations on which the divergence for both capsid proteins was based occurred in the past 30 years. Based on these findings, it was concluded that PPV variants are continuously evolving and that vaccines, which are based mainly on strains isolated about 30 years ago, should perhaps be updated.
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Tillier, Elisabeth R. M., and Richard A. Collins. "High Apparent Rate of Simultaneous Compensatory Base-Pair Substitutions in Ribosomal RNA." Genetics 148, no. 4 (April 1, 1998): 1993–2002. http://dx.doi.org/10.1093/genetics/148.4.1993.
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Abstract We present a model for the evolution of paired bases in RNA sequences. The new model allows for the instantaneous rate of substitution of both members of a base pair in a compensatory substitution (e.g., A-U→G-C) and expands our previous work by allowing for unpaired bases or noncanonical pairs. We implemented the model with distance and maximum likelihood methods to estimate the rates of simultaneous substitution of both bases, αd, vs. rates of substitution of individual bases, αs in rRNA. In the rapidly evolving D2 expansion segments of Drosophila large subunit rRNA, we estimate a low ratio of αd/αs, indicating that most compensatory substitutions involve a G-U intermediate. In contrast, we find a surprisingly high ratio of αd/αs in the core small subunit rRNA, indicating that the evolution of the slowly evolving rRNA sequences is modeled much more accurately if simultaneous substitution of both members of a base pair is allowed to occur approximately as often as substitution of individual bases. Using simulations, we have ruled out several potential sources of error in the estimation of αd/αs. We conclude that in the core rRNA sequences compensatory substitutions can be fixed so rapidly as to appear to be instantaneous.
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Takano, Toshiyuki S. "Rate Variation of DNA Sequence Evolution in the Drosophila Lineages." Genetics 149, no. 2 (June 1, 1998): 959–70. http://dx.doi.org/10.1093/genetics/149.2.959.
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Abstract Rate constancy of DNA sequence evolution was examined for three species of Drosophila, using two samples: the published sequences of eight genes from regions of the normal recombination rates and new data of the four AS-C (ac, sc, l'sc and ase) and ci genes. The AS-C and ci genes were chosen because these genes are located in the regions of very reduced recombination in Drosophila melanogaster and their locations remain unchanged throughout the entire lineages involved, yielding less effect of ancestral polymorphism in the study of rate constancy. The synonymous substitution pattern of the three lineages was found to be erratic in both samples. The dispersion index for replacement substitution was relatively high for the per, G6pd and ac genes. A significant heterogeneity was found in the number of synonymous substitutions in the three lineages between the two samples of genes with different recombination rates. This is partly due to a lack of the lineage effect in the D. melanogaster and Drosophila simulans lineages in the AS-C and ci genes in contrast to Akashi's observation of genes in regions of normal recombination. The higher codon bias in Drosophila yakuba as compared with D. melanogaster and D. simulans was observed in the four AS-C genes, which suggests change(s) in action of natural selection involved in codon usage on these genes. Fluctuating selection intensity may also be responsible for the observed locus-lineage interaction effects in synonymous substitution.
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Stephan, Wolfgang. "The Rate of Compensatory Evolution." Genetics 144, no. 1 (September 1, 1996): 419–26. http://dx.doi.org/10.1093/genetics/144.1.419.
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Abstract A two-locus model is presented to analyze the evolution of compensatory mutations occurring in stems of RNA secondary structures. Single mutations are assumed to be deleterious but harmless (neutral) in appropriate combinations. In proceeding under mutation pressure, natural selection and genetic drift from one fitness peak to another one, a population must therefore pass through a valley of intermediate deleterious states of individual fitness. The expected time for this transition is calculated using diffusion theory. The rate of compensatory evolution, kc, is then defined as the inverse of the expected transition time. When selection against deleterious single mutations is strong, kc, depends on the recombination fraction r between the two loci. Recombination generally reduces the rate of compensatory evolution because it breaks up favorable combinations of double mutants. For complete linkage, kc, is given by the rate at which favorable combinations of double mutantS are produced by compensatory mutation. For r > 0, kc, decreases exponentially with r. In contrast, kc, becomes independent of r for weak selection. We discuss the dynamics of evolutionary substitutions of compensatory mutants in relation to Wright'S shifting balance theory of evolution and use our results to analyze the substitution process in helices of mRNA secondary structures.
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Bielawski, Joseph P., Katherine A. Dunn, and Ziheng Yang. "Rates of Nucleotide Substitution and Mammalian Nuclear Gene Evolution: Approximate and Maximum-Likelihood Methods Lead to Different Conclusions." Genetics 156, no. 3 (November 1, 2000): 1299–308. http://dx.doi.org/10.1093/genetics/156.3.1299.
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Abstract Rates and patterns of synonymous and nonsynonymous substitutions have important implications for the origin and maintenance of mammalian isochores and the effectiveness of selection at synonymous sites. Previous studies of mammalian nuclear genes largely employed approximate methods to estimate rates of nonsynonymous and synonymous substitutions. Because these methods did not account for major features of DNA sequence evolution such as transition/transversion rate bias and unequal codon usage, they might not have produced reliable results. To evaluate the impact of the estimation method, we analyzed a sample of 82 nuclear genes from the mammalian orders Artiodactyla, Primates, and Rodentia using both approximate and maximum-likelihood methods. Maximum-likelihood analysis indicated that synonymous substitution rates were positively correlated with GC content at the third codon positions, but independent of nonsynonymous substitution rates. Approximate methods, however, indicated that synonymous substitution rates were independent of GC content at the third codon positions, but were positively correlated with nonsynonymous rates. Failure to properly account for transition/transversion rate bias and unequal codon usage appears to have caused substantial biases in approximate estimates of substitution rates.
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Zhang, Jianzhi, and Xun Gu. "Correlation Between the Substitution Rate and Rate Variation Among Sites in Protein Evolution." Genetics 149, no. 3 (July 1, 1998): 1615–25. http://dx.doi.org/10.1093/genetics/149.3.1615.
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Abstract It is well known that the rate of amino acid substitution varies among different proteins and among different sites of a protein. It is, however, unclear whether the extent of rate variation among sites of a protein and the mean substitution rate of the protein are correlated. We used two approaches to analyze orthologous protein sequences of 51 nuclear genes of vertebrates and 13 mitochondrial genes of mammals. In the first approach, no assumptions of the distribution of the rate variation among sites were made, and in the second approach, the gamma distribution was assumed. Through both approaches, we found a negative correlation between the extent of among-site rate variation and the average substitution rate of a protein. That is, slowly evolving proteins tend to have a high level of rate variation among sites, and vice versa. We found this observation consistent with a simple model of the neutral theory where most sites are either invariable or neutral. We conclude that the correlation is a general feature of protein evolution and discuss its implications in statistical tests of positive Darwinian selection and molecular time estimation of deep divergences.
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Duffy, Siobain, and Edward C. Holmes. "Phylogenetic Evidence for Rapid Rates of Molecular Evolution in the Single-Stranded DNA Begomovirus Tomato Yellow Leaf Curl Virus." Journal of Virology 82, no. 2 (October 31, 2007): 957–65. http://dx.doi.org/10.1128/jvi.01929-07.
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ABSTRACT Geminiviruses are devastating viruses of plants that possess single-stranded DNA (ssDNA) DNA genomes. Despite the importance of this class of phytopathogen, there have been no estimates of the rate of nucleotide substitution in the geminiviruses. We report here the evolutionary rate of the tomato yellow leaf curl disease-causing viruses, an intensively studied group of monopartite begomoviruses. Sequences from GenBank, isolated from diseased plants between 1988 and 2006, were analyzed using Bayesian coalescent methods. The mean genomic substitution rate was estimated to be 2.88 × 10−4 nucleotide substitutions per site per year (subs/site/year), although this rate could be confounded by frequent recombination within Tomato yellow leaf curl virus genomes. A recombinant-free data set comprising the coat protein (V1) gene in isolation yielded a similar mean rate (4.63 × 10−4 subs/site/year), validating the order of magnitude of genomic substitution rate for protein-coding regions. The intergenic region, which is known to be more variable, was found to evolve even more rapidly, with a mean substitution rate of ∼1.56 × 10−3 subs/site/year. Notably, these substitution rates, the first reported for a plant DNA virus, are in line with those estimated previously for mammalian ssDNA viruses and RNA viruses. Our results therefore suggest that the high evolutionary rate of the geminiviruses is not primarily due to frequent recombination and may explain their ability to emerge in novel hosts.
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Grigoras, Ioana, Tatiana Timchenko, Ana Grande-Pérez, Lina Katul, Heinrich-Josef Vetten, and Bruno Gronenborn. "High Variability and Rapid Evolution of a Nanovirus." Journal of Virology 84, no. 18 (June 30, 2010): 9105–17. http://dx.doi.org/10.1128/jvi.00607-10.
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ABSTRACT Nanoviruses are multipartite single-stranded DNA (ssDNA) plant viruses that cause important diseases of leguminous crops and banana. Little has been known about the variability and molecular evolution of these viruses. Here we report on the variability of faba bean necrotic stunt virus (FBNSV), a nanovirus from Ethiopia. We found mutation frequencies of 7.52 × 10−4 substitutions per nucleotide in a field population of the virus and 5.07 × 10−4 substitutions per nucleotide in a laboratory-maintained population derived thereof. Based on virus propagation for a period of more than 2 years, we determined a nucleotide substitution rate of 1.78 × 10−3 substitutions per nucleotide per year. This high molecular evolution rate places FBNSV, as a representative of the family Nanoviridae, among the fastest-evolving ssDNA viruses infecting plants or vertebrates.
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Mugal, C. F., J. B. W. Wolf, H. H. von Grünberg, and H. Ellegren. "Conservation of Neutral Substitution Rate and Substitutional Asymmetries in Mammalian Genes." Genome Biology and Evolution 2 (January 1, 2010): 19–28. http://dx.doi.org/10.1093/gbe/evp056.
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Hartmann, Marike, and G. Brian Golding. "Searching for Substitution Rate Heterogeneity." Molecular Phylogenetics and Evolution 9, no. 1 (February 1998): 64–71. http://dx.doi.org/10.1006/mpev.1997.0446.
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Moutinho, Ana Filipa, Thomas Bataillon, and Julien Y. Dutheil. "Variation of the adaptive substitution rate between species and within genomes." Evolutionary Ecology 34, no. 3 (December 14, 2019): 315–38. http://dx.doi.org/10.1007/s10682-019-10026-z.
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AbstractThe importance of adaptive mutations in molecular evolution is extensively debated. Recent developments in population genomics allow inferring rates of adaptive mutations by fitting a distribution of fitness effects to the observed patterns of polymorphism and divergence at sites under selection and sites assumed to evolve neutrally. Here, we summarize the current state-of-the-art of these methods and review the factors that affect the molecular rate of adaptation. Several studies have reported extensive cross-species variation in the proportion of adaptive amino-acid substitutions (α) and predicted that species with larger effective population sizes undergo less genetic drift and higher rates of adaptation. Disentangling the rates of positive and negative selection, however, revealed that mutations with deleterious effects are the main driver of this population size effect and that adaptive substitution rates vary comparatively little across species. Conversely, rates of adaptive substitution have been documented to vary substantially within genomes. On a genome-wide scale, gene density, recombination and mutation rate were observed to play a role in shaping molecular rates of adaptation, as predicted under models of linked selection. At the gene level, it has been reported that the gene functional category and the macromolecular structure substantially impact the rate of adaptive mutations. Here, we deliver a comprehensive review of methods used to infer the molecular adaptive rate, the potential drivers of adaptive evolution and how positive selection shapes molecular evolution within genes, across genes within species and between species.
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Kupczok, Anne, and Tal Dagan. "Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage." Viruses 11, no. 8 (August 6, 2019): 720. http://dx.doi.org/10.3390/v11080720.
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Cyanophages are characterized by vast genomic diversity and the formation of stable ecotypes over time. The evolution of phage diversity includes vertical processes, such as mutation, and horizontal processes, such as recombination and gene transfer. Here, we study the contribution of vertical and horizontal processes to short-term evolution of marine cyanophages. Analyzing time series data of Synechococcus-infecting Myoviridae ecotypes spanning up to 17 years, we found a high contribution of recombination relative to mutation (r/m) in all ecotypes. Additionally, we found a molecular clock of substitution and recombination in one ecotype, RIM8. The estimated RIM8 evolutionary rates are 2.2 genome-wide substitutions per year (1.275 × 10−5 substitutions/site/year) and 29 genome-wide nucleotide alterations due to recombination per year. We found 26 variable protein families, of which only two families have a predicted functional annotation, suggesting that they are auxiliary metabolic genes with bacterial homologs. A comparison of our rate estimates to other phage evolutionary rate estimates in the literature reveals a negative correlation of phage substitution rates with their genome size. A comparison to evolutionary rates in bacterial organisms further shows that phages have high rates of mutation and recombination compared to their bacterial hosts. We conclude that the increased recombination rate in phages likely contributes to their vast genomic diversity.
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Gillespie, J. H. "Substitution processes in molecular evolution. I. Uniform and clustered substitutions in a haploid model." Genetics 134, no. 3 (July 1, 1993): 971–81. http://dx.doi.org/10.1093/genetics/134.3.971.
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Abstract A computer simulation of the process of nucleotide substitutions in a finite haploid population subject to selection in a randomly fluctuating environment provides a number of unexpected results. For rapidly fluctuating environments, substitutions are more regular than random. A small mutation-rate approximation is used to explain the regularity. The explanation does not depend heavily on the particulars of the haploid model, leading to the conjecture that many symmetrical models of molecular evolution with rapidly changing parameters may exhibit substitutions that are more regular than random. When fitnesses change very slowly, the simulation shows that substitutions are more clumped than random. Here a small-mutation approximation shows that the clustering is due to the increase in fitness that accompanies each successive substitution with a consequent lowering of the effective mutation rate. The two observations taken together suggest that the common observation that amino acid substitutions are clustered in time is due to the presence of parameters that change very slowly.
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Yang, Z. "A space-time process model for the evolution of DNA sequences." Genetics 139, no. 2 (February 1, 1995): 993–1005. http://dx.doi.org/10.1093/genetics/139.2.993.
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Abstract We describe a model for the evolution of DNA sequences by nucleotide substitution, whereby nucleotide sites in the sequence evolve over time, whereas the rates of substitution are variable and correlated over sites. The temporal process used to describe substitutions between nucleotides is a continuous-time Markov process, with the four nucleotides as the states. The spatial process used to describe variation and dependence of substitution rates over sites is based on a serially correlated gamma distribution, i.e., an auto-gamma model assuming Markov-dependence of rates at adjacent sites. To achieve computational efficiency, we use several equal-probability categories to approximate the gamma distribution, and the result is an auto-discrete-gamma model for rates over sites. Correlation of rates at sites then is modeled by the Markov chain transition of rates at adjacent sites from one rate category to another, the states of the chain being the rate categories. Two versions of nonparametric models, which place no restrictions on the distributional forms of rates for sites, also are considered, assuming either independence or Markov dependence. The models are applied to data of a segment of mitochondrial genome from nine primate species. Model parameters are estimated by the maximum likelihood method, and models are compared by the likelihood ratio test. Tremendous variation of rates among sites in the sequence is revealed by the analyses, and when rate differences for different codon positions are appropriately accounted for in the models, substitution rates at adjacent sites are found to be strongly (positively) correlated. Robustness of the results to uncertainty of the phylogenetic tree linking the species is examined.
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Hightower, Robin C., and Richard B. Meagher. "THE MOLECULAR EVOLUTION OF ACTIN." Genetics 114, no. 1 (September 1, 1986): 315–32. http://dx.doi.org/10.1093/genetics/114.1.315.
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ABSTRACT We have investigated the molecular evolution of plant and nonplant actin genes comparing nucleotide and amino acid sequences of 20 actin genes. Nucleotide changes resulting in amino acid substitutions (replacement substitutions) ranged from 3-7% for all pairwise comparisons of animal actin genes with the following exceptions. Comparisons between higher animal muscle actin gene sequences and comparisons between higher animal cytoplasmic actin gene sequences indicated <3% divergence. Comparisons between plant and nonplant actin genes revealed, with two exceptions, 11-15% replacement substitution. In the analysis of plant actins, replacement substitution between soybean actin genes SAc1, SAc3, SAc4 and maize actin gene MAc1 ranged from 8-10%, whereas these members within the soybean actin gene family ranged from 6-9% replacement substitution. The rate of sequence divergence of plant actin sequences appears to be similar to that observed for animal actins. Furthermore, these and other data suggest that the plant actin gene family is ancient and that the families of soybean and maize actin genes have diverged from a single common ancestral plant actin gene that originated long before the divergence of monocots and dicots. The soybean actin multigene family encodes at least three classes of actin. These classes each contain a pair of actin genes that have been designated kappa (SAc1, SAc6), lambda (SAc2, SAc4) and mu (SAc3, SAc7). The three classes of soybean actin are more divergent in nucleotide sequence from one another than higher animal cytoplasmic actin is divergent from muscle actin. The location and distribution of amino acid changes were compared between actin proteins from all sources. A comparison of the hydropathy of all actin sequences, except from Oxytricha, indicated a strong similarity in hydropathic character between all plant and nonplant actins despite the greater number of replacement substitutions in plant actins. These protein sequence comparisons are discussed with respect to the demonstrated and implicated roles of actin in plants and animals, as well as the tissue-specific expression of actin.
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Davis, Patricia L., Edward C. Holmes, Florence Larrous, Wim H. M. Van der Poel, Kirsten Tjørnehøj, Wladimir J. Alonso, and Hervé Bourhy. "Phylogeography, Population Dynamics, and Molecular Evolution of European Bat Lyssaviruses." Journal of Virology 79, no. 16 (August 15, 2005): 10487–97. http://dx.doi.org/10.1128/jvi.79.16.10487-10497.2005.
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ABSTRACT European bat lyssaviruses types 1 and 2 (EBLV-1 and EBLV-2) are widespread in Europe, although little is known of their evolutionary history. We undertook a comprehensive sequence analysis to infer the selection pressures, rates of nucleotide substitution, age of genetic diversity, geographical origin, and population growth rates of EBLV-1. Our study encompassed data from 12 countries collected over a time span of 35 years and focused on the glycoprotein (G) and nucleoprotein (N) genes. We show that although the two subtypes of EBLV-1—EBLV-1a and EBLV-1b—have both grown at a low exponential rate since their introduction into Europe, they have differing population structures and dispersal patterns. Furthermore, there were strong constraints against amino acid change in both EBLV-1 and EBLV-2, as reflected in a low ratio of nonsynonymous to synonymous substitutions per site, particularly in EBLV-1b. Our inferred rate of nucleotide substitution in EBLV-1, approximately 5 × 10−5 substitutions per site per year, was also one of the lowest recorded for RNA viruses and implied that the current genetic diversity in the virus arose 500 to 750 years ago. We propose that the slow evolution of EBLVs reflects their distinctive epidemiology in bats, where they occupy a relatively stable fitness peak.
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Gillespie, J. H. "Substitution processes in molecular evolution. III. Deleterious alleles." Genetics 138, no. 3 (November 1, 1994): 943–52. http://dx.doi.org/10.1093/genetics/138.3.943.
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Abstract The substitution processes for various models of deleterious alleles are examined using computer simulations and mathematical analyses. Most of the work focuses on the house-of-cards model, which is a popular model of deleterious allele evolution. The rate of substitution is shown to be a concave function of the strength of selection as measured by alpha = 2N sigma, where N is the population size and sigma is the standard deviation of fitness. For alpha < 1, the house-of-cards model is essentially a neutral model; for alpha > 4, the model ceases to evolve. The stagnation for large alpha may be understood by appealing to the theory of records. The house-of-cards model evolves to a state where the vast majority of all mutations are deleterious, but precisely one-half of those mutations that fix are deleterious (the other half are advantageous). Thus, the model is not a model of exclusively deleterious evolution as is frequently claimed. It is argued that there are no biologically reasonable models of molecular evolution where the vast majority of all substitutions are deleterious. Other models examined include the exponential and gamma shift models, the Hartl-Dykhuizen-Dean (HDD) model, and the optimum model. Of all those examined, only the optimum and HDD models appear to be reasonable candidates for silent evolution. None of the models are viewed as good candidates for protein evolution, as none are both biologically reasonable and exhibit the variability in substitutions commonly observed in protein sequence data.
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Kaneko, Maki, Yoko Satta, Etsuko T. Matsuura, and Sadao I. Chigusa. "Evolution of the mitochondrial ATPase 6 gene in Drosophila: unusually high level of polymorphism in D. melanogaster." Genetical Research 61, no. 3 (June 1993): 195–204. http://dx.doi.org/10.1017/s0016672300031360.
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SummaryWe have determined 1990 bp mitochondrial DNA sequence which extends from 3′ end of the cytochrome oxidase subunit I (COI) gene to 5′ end of the COIII gene from two sibling species of Drosophila, D. simulans and D. mauritiana. Analyses of the sequences and part of the NADH dehydrogenase subunit 2 gene and the COI gene together with those from D. melanogaster and D. yakuba revealed that amino-acid substitution rate of the ATPase 6 gene seems to be higher in some strains of D. melanogaster than in the other species. High level of amino-acid polymorphism in this gene was observed in D. melanogaster. Synonymous substitution rate is relatively constant in all the genes examined, suggesting that mutation rate is not higher in the ATPase 6 gene of D. melanogaster. The amino-acid substitutions found specifically in D. melanogaster are at the sites which are not conserved among mammals, yeast and E. coli. These sites of the ATPase 6 gene might lose the selective constraint in D. melanogaster, and the amino-acid substitutions can be explained by neutral mutations and random genetic drift.
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Ryynänen, Heikki J., and Craig R. Primmer. "Varying signals of the effects of natural selection during teleost growth hormone gene evolution." Genome 49, no. 1 (January 1, 2006): 42–53. http://dx.doi.org/10.1139/g05-079.
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The growth hormone (GH) gene of teleost fish exhibits a higher degree of variability compared with other vertebrate groups. However, the different selective constraints at the sequence level are not well understood. In this study, maximum-likelihood (ML) models of codon substitutions were used to investigate Darwinian adaptive evolution of the GH gene in teleost fishes. Complete GH gene sequences of 54 fish species were classified into 4 orders, and the variable nature of GH was examined by determining the dN and dS rate variation and the rates of molecular evolution for each teleost order. The results indicate that although the overall evolution rate for teleost GH is high ((1.15 ± 0.01) × 10–9 substitutions/(aa site·y)) compared with the "slow phases" in mammals ((0.21 to 0.28 ± 0.05) × 10–9), the vital structure of this gene has been retained. While the majority of the amino acid changes appear to be due to relaxation of purifying selection, some positively selected sites were detected in regions with no specifically identified role in protein function. The positively selected regions observed in salmoniformes lineage suggests a possible role for positive selection driving functional divergence in paralogous forms of the GH gene after whole-genome duplication in this lineage.Key words: teleost fish, growth hormone, positive selection, synonymous substitution, non-synonymous substitution, molecular evolution.
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Murrell, Anna, Susan J. Dobson, David E. Walter, Nick J. H. Campbell, Renfu Shao, and Stephen C. Barker. "Relationships among the three major lineages of the Acari (Arthropoda:Arachnida) inferred from small subunit rRNA: paraphyly of the Parasitiformes with respect to the Opilioacariformes and relative rates of nucleotide substitution." Invertebrate Systematics 19, no. 5 (2005): 383. http://dx.doi.org/10.1071/is05027.
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We inferred phylogeny among the three major lineages of the Acari (mites) from the small subunit rRNA gene. Our phylogeny indicates that the Opilioacariformes is the sister-group to the Ixodida+Holothyrida, not the Ixodida+Mesostigmata+Holothyrida, as previously thought. Support for this relationship increased when sites with the highest rates of nucleotide substitution, and thus the greatest potential for saturation with nucleotide substitutions, were removed. Indeed, the increase in support (and resolution) was despite a 70% reduction in the number of parsimony-informative sites from 408 to 115. This shows that rather than ‘noisy’ sites having no impact on resolution of deep branches, ‘noisy’ sites have the potential to obscure phylogenetic relationships. The arrangement, Ixodida+Holothyrida+Opilioacariformes, however, may be an artefact of long-branch attraction since relative-rate tests showed that the Mesostigmata have significantly faster rates of nucleotide substitution than other parasitiform mites. Thus, the fast rates of nucleotide substitution of the Mesostigmata might have caused the Mesostigmata to be attracted to the outgroup in our trees. We tested the hypothesis that the high rate of nucleotide substitution in some mites was related to their short generation times. The Acari species that have high nucleotide substitution rates usually have short generation times; these mites also tend to be more active and thus have higher metabolic rates than other mites. Therefore, more than one factor may affect the rate of nucleotide substitution in these mites.
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McAllister, Bryant F., and Gilean A. T. McVean. "Neutral Evolution of the Sex-Determining Gene transformer in Drosophila." Genetics 154, no. 4 (April 1, 2000): 1711–20. http://dx.doi.org/10.1093/genetics/154.4.1711.
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Abstract The amino acid sequence of the transformer (tra) gene exhibits an extremely rapid rate of evolution among Drosophila species, although the gene performs a critical step in sex determination. These changes in amino acid sequence are the result of either natural selection or neutral evolution. To differentiate between selective and neutral causes of this evolutionary change, analyses of both intraspecific and interspecific patterns of molecular evolution of tra gene sequences are presented. Sequences of 31 tra alleles were obtained from Drosophila americana. Many replacement and silent nucleotide variants are present among the alleles; however, the distribution of this sequence variation is consistent with neutral evolution. Sequence evolution was also examined among six species representative of the genus Drosophila. For most lineages and most regions of the gene, both silent and replacement substitutions have accumulated in a constant, clock-like manner. In exon 3 of D. virilis and D. americana we find evidence for an elevated rate of nonsynonymous substitution, but no statistical support for a greater rate of nonsynonymous relative to synonymous substitutions. Both levels of analysis of the tra sequence suggest that, although the gene is evolving at a rapid pace, these changes are neutral in function.
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Gillooly, James F., Michael W. McCoy, and Andrew P. Allen. "Effects of metabolic rate on protein evolution." Biology Letters 3, no. 6 (October 2, 2007): 655–60. http://dx.doi.org/10.1098/rsbl.2007.0403.
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Since the modern evolutionary synthesis was first proposed early in the twentieth century, attention has focused on assessing the relative contribution of mutation versus natural selection on protein evolution. Here we test a model that yields general quantitative predictions on rates of protein evolution by combining principles of individual energetics with Kimura's neutral theory. The model successfully predicts much of the heterogeneity in rates of protein evolution for diverse eukaryotes (i.e. fishes, amphibians, reptiles, birds, mammals) from different thermal environments. Data also show that the ratio of non-synonymous to synonymous nucleotide substitution is independent of body size, and thus presumably of effective population size. These findings indicate that rates of protein evolution are largely controlled by mutation rates, which in turn are strongly influenced by individual metabolic rate.
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dos Reis, Mario. "How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher–Wright mutation–selection framework." Biology Letters 11, no. 4 (April 2015): 20141031. http://dx.doi.org/10.1098/rsbl.2014.1031.
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First principles of population genetics are used to obtain formulae relating the non-synonymous to synonymous substitution rate ratio to the selection coefficients acting at codon sites in protein-coding genes. Two theoretical cases are discussed and two examples from real data (a chloroplast gene and a virus polymerase) are given. The formulae give much insight into the dynamics of non-synonymous substitutions and may inform the development of methods to detect adaptive evolution.
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Ghatak, V., and P. D. Ghosh. "Studying molecular evolution using tools of bioinformatics: an example from maize starch biosynthetic pathway." NBU Journal of Plant Sciences 5, no. 1 (2011): 1–5. http://dx.doi.org/10.55734/nbujps.2011.v05i01.001.
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Various tools and techniques of bioinformatics are used to reveal the evolutionary pattern and chronology of different phylogenetic events in the evolutionary history of an organism. n maize, shrunken, brittle, waxy and sugary mutants all results from anomalies in the starch biosynthetic pathway. The genes responsible are shl, bt2,wxl and sul respectively. The present article explores and depicts an outline of computer application based methods adopted in a standard molecular phylogenetic analysis using sequence data of these gene products controlling different steps of maize starch biosynthetic pathway. Several such methods namely MSA, PSI-BLAST, Maximum Likelihood analysis and UPGMA analysis reveals that shrunkenl, waxyl and sugaryl have evolutionary rates ranging in between 0.001-0.003 substitutions per Site. Non-synonymous substitution (as polymorphism is analysed using protein sequences) substitution rate is much slower in brittle2 (0.0006). The divergence times between the ancestors of Sorghum and Maize teosinte lineage has been calculated from these non-synonymous substitution rates. MEME analyses and distribution of motifs in these sequences and their homologues suggest changes (duplication and rearrangements) in the genetic material after Sorghum-maize split.
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Savill, Nicholas J., David C. Hoyle, and Paul G. Higgs. "RNA Sequence Evolution With Secondary Structure Constraints: Comparison of Substitution Rate Models Using Maximum-Likelihood Methods." Genetics 157, no. 1 (January 1, 2001): 399–411. http://dx.doi.org/10.1093/genetics/157.1.399.
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Abstract We test models for the evolution of helical regions of RNA sequences, where the base pairing constraint leads to correlated compensatory substitutions occurring on either side of the pair. These models are of three types: 6-state models include only the four Watson-Crick pairs plus GU and UG; 7-state models include a single mismatch state that combines all of the 10 possible mismatches; 16-state models treat all mismatch states separately. We analyzed a set of eubacterial ribosomal RNA sequences with a well-established phylogenetic tree structure. For each model, the maximum-likelihood values of the parameters were obtained. The models were compared using the Akaike information criterion, the likelihood-ratio test, and Cox’s test. With a high significance level, models that permit a nonzero rate of double substitutions performed better than those that assume zero double substitution rate. Some models assume symmetry between GC and CG, between AU and UA, and between GU and UG. Models that relaxed this symmetry assumption performed slightly better, but the tests did not all agree on the significance level. The most general time-reversible model significantly outperformed any of the simplifications. We consider the relative merits of all these models for molecular phylogenetics.
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Lehtonen, Jussi, and Robert Lanfear. "Generation time, life history and the substitution rate of neutral mutations." Biology Letters 10, no. 11 (November 2014): 20140801. http://dx.doi.org/10.1098/rsbl.2014.0801.
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Our understanding of molecular evolution is hampered by a lack of quantitative predictions about how life-history (LH) traits should correlate with substitution rates. Comparative studies have shown that neutral substitution rates vary substantially between species, and evidence shows that much of this diversity is associated with variation in LH traits. However, while these studies often agree, some unexplained and contradictory results have emerged. Explaining these results is difficult without a clear theoretical understanding of the problem. In this study, we derive predictions for the relationships between LH traits and substitution rates in iteroparous species by using demographic theory to relate commonly measured life-history traits to genetic generation time, and by implication to neutral substitution rates. This provides some surprisingly simple explanations for otherwise confusing patterns, such as the association between fecundity and substitution rates. The same framework can be applied to more complex life histories if full life-tables are available.
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Berbee, Mary L., and John W. Taylor. "Dating the evolutionary radiations of the true fungi." Canadian Journal of Botany 71, no. 8 (August 1, 1993): 1114–27. http://dx.doi.org/10.1139/b93-131.
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In this paper we construct a relative time scale for the origin and radiation of major lineages of the true fungi, using the 18S ribosomal RNA gene sequence data of 37 fungal species, and then calibrate the time scale using fossil evidence. Of the sequences, 28 were from the literature or data banks and the remaining 9 are new. To estimate the order of origin of fungal lineages we reconstructed the phylogeny of the fungi using aligned sequence data. To compensate for the differences in nucleotide substitution rates among various fungal lineages, we normalized the pairwise substitution data before estimating the relative timing of fungal divergences. We divided the fungi into nine groups. We then calculated the average percent substitution for each group, and also the average for all the groups, for the time period beginning when the fungi diverged from a common ancestor and ending at the present. We used the ratios of group-specific percent substitutions to the average percent substitution to normalize our pairwise substitution data matrix. To infer the relative timing of the origin of lineages we superimposed the normalized percentages of nucleotide substitutions onto the parsimony-based phylogeny. Calibrating the rate of sequence change involved relating the normalized percent substitution associated with phylogenetic events to fungal fossils, the ages of fungus hosts, and ages of symbionts. These calibration points were consistent with a substitution rate of 1% per lineage per 100 Ma. Based on phylogeny and calibrated percent substitution, the terrestrial fungi diverged from the chytrids approximately 550 Ma ago. After plants invaded the land approximately 400 Ma ago, ascomycetes split from basidiomycetes. Mushrooms, many ascomycetous yeasts, and common molds in the genera Penicillium and Aspergillus may have evolved after the origin of angiosperm plants and in the last 200 Ma. Key words: fungus evolution, molecular clock, ascomycete phylogeny, basidiomycete phylogeny, 18S rRNA.
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Easteal, S. "The pattern of mammalian evolution and the relative rate of molecular evolution." Genetics 124, no. 1 (January 1, 1990): 165–73. http://dx.doi.org/10.1093/genetics/124.1.165.
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Abstract The rates of nucleotide substitution at four genes in four orders of eutherian mammals are compared in relative rate tests using marsupial orthologs for reference. There is no evidence of systematic variation in evolutionary rate among the orders. The sequences are used to reconstruct the phylogeny of the orders using maximum likelihood, parsimony and compatibility methods. A branching order of rodent then ungulate then primate and lagomorph is overwhelmingly indicated. The nodes of the nucleotide based cladograms are widely separated in relation to the total lengths of the branches. The assumption of a star phylogeny that underlies Kimura's test for molecular evolutionary rate variation is shown to be invalid for eutherian mammals. Excess variance in nucleotide or amino acid differences between mammalian orders, above that predicted by neutral theory is explained better by variation in divergence time than by variation in evolutionary rate.
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Burskaia, Valentina, Sergey Naumenko, Mikhail Schelkunov, Daria Bedulina, Tatyana Neretina, Alexey Kondrashov, Lev Yampolsky, and Georgii A. Bazykin. "Excessive Parallelism in Protein Evolution of Lake Baikal Amphipod Species Flock." Genome Biology and Evolution 12, no. 9 (July 11, 2020): 1493–503. http://dx.doi.org/10.1093/gbe/evaa138.
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Abstract Repeated emergence of similar adaptations is often explained by parallel evolution of underlying genes. However, evidence of parallel evolution at amino acid level is limited. When the analyzed species are highly divergent, this can be due to epistatic interactions underlying the dynamic nature of the amino acid preferences: The same amino acid substitution may have different phenotypic effects on different genetic backgrounds. Distantly related species also often inhabit radically different environments, which makes the emergence of parallel adaptations less likely. Here, we hypothesize that parallel molecular adaptations are more prevalent between closely related species. We analyze the rate of parallel evolution in genome-size sets of orthologous genes in three groups of species with widely ranging levels of divergence: 46 species of the relatively recent lake Baikal amphipod radiation, a species flock of very closely related cichlids, and a set of significantly more divergent vertebrates. Strikingly, in genes of amphipods, the rate of parallel substitutions at nonsynonymous sites exceeded that at synonymous sites, suggesting rampant selection driving parallel adaptation. At sites of parallel substitutions, the intraspecies polymorphism is low, suggesting that parallelism has been driven by positive selection and is therefore adaptive. By contrast, in cichlids, the rate of nonsynonymous parallel evolution was similar to that at synonymous sites, whereas in vertebrates, this rate was lower than that at synonymous sites, indicating that in these groups of species, parallel substitutions are mainly fixed by drift.
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Ochman, Howard, and Allan C. Wilson. "Evolution in bacteria: Evidence for a universal substitution rate in cellular genomes." Journal of Molecular Evolution 26, no. 1-2 (November 1987): 74–86. http://dx.doi.org/10.1007/bf02111283.
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Knies, J. L., K. K. Dang, T. J. Vision, N. G. Hoffman, R. Swanstrom, and C. L. Burch. "Compensatory Evolution in RNA Secondary Structures Increases Substitution Rate Variation among Sites." Molecular Biology and Evolution 25, no. 8 (April 23, 2008): 1778–87. http://dx.doi.org/10.1093/molbev/msn130.
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Ochman, H., and A. C. Wilson. "Evolution in bacteria: Evidence for a universal substitution rate in cellular genomes." Journal of Molecular Evolution 26, no. 4 (December 1987): 377. http://dx.doi.org/10.1007/bf02101157.
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Purugganan, M. D., and S. R. Wessler. "Molecular evolution of the plant R regulatory gene family." Genetics 138, no. 3 (November 1, 1994): 849–54. http://dx.doi.org/10.1093/genetics/138.3.849.
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Abstract Anthocyanin pigmentation patterns in different plant species are controlled in part by members of the myc-like R regulatory gene family. We have examined the molecular evolution of this gene family in seven plant species. Three regions of the R protein show sequence conservation between monocot and dicot R genes. These regions encode the basic helix-loop-helix domain, as well as conserved N-terminal and C-terminal domains; mean replacement rates for these conserved regions are 1.02 x 10(-9) nonsynonymous nucleotide substitutions per site per year. More than one-half of the protein, however, is diverging rapidly, with nonsynonymous substitution rates of 4.08 x 10(-9) substitutions per site per year. Detailed analysis of R homologs within the grasses (Poaceae) confirm that these variable regions are indeed evolving faster than the flanking conserved domains. Both nucleotide substitutions and small insertion/deletions contribute to the diversification of the variable regions within these regulatory genes. These results demonstrate that large tracts of sequence in these regulatory loci are evolving at a fairly rapid rate.
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Morton, Brian R. "Do Noncoding and Coding Sites in Angiosperm Chloroplast DNA Have Different Mutation Processes?" Genes 14, no. 1 (January 5, 2023): 148. http://dx.doi.org/10.3390/genes14010148.
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Fourfold degenerate sites within coding regions and intergenic sites have both been used as estimates of neutral evolution. In chloroplast DNA, the pattern of substitution at intergenic sites is strongly dependent on the composition of the surrounding hexanucleotide composed of the three base pairs on each side, which suggests that the mutation process is highly context-dependent in this genome. This study examines the context-dependency of substitutions at fourfold degenerate sites in protein-coding regions and compares the pattern to what has been observed at intergenic sites. Overall, there is strong similarity between the two types of sites, but there are some intriguing differences. One of these is that substitutions of G and C are significantly higher at fourfold degenerate sites across a range of contexts. In fact, A → T and T → A substitutions are the only substitution types that occur at a lower rate at fourfold degenerate sites. The data are not consistent with selective constraints being responsible for the difference in substitution patterns between intergenic and fourfold degenerate sites. Rather, it is suggested that the difference may be a result of different epigenetic modifications that result in slightly different mutation patterns in coding and intergenic DNA.
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Johnson, Kevin P., Julie M. Allen, Brett P. Olds, Lawrence Mugisha, David L. Reed, Ken N. Paige, and Barry R. Pittendrigh. "Rates of genomic divergence in humans, chimpanzees and their lice." Proceedings of the Royal Society B: Biological Sciences 281, no. 1777 (February 22, 2014): 20132174. http://dx.doi.org/10.1098/rspb.2013.2174.
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The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their hosts when comparing single genes. However, the variation in this relative rate of molecular evolution across different genes in the genome is unknown. We compared the rate of DNA sequence divergence between humans, chimpanzees and their ectoparasitic lice for 1534 protein-coding genes across their genomes. The rate of DNA substitution in these orthologous genes was on average 14 times faster for lice than for humans and chimpanzees. In addition, these rates were positively correlated across genes. Because this correlation only occurred for substitutions that changed the amino acid, this pattern is probably produced by similar functional constraints across the same genes in humans, chimpanzees and their ectoparasites.
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Dunn, Katherine A., Joseph P. Bielawski, and Ziheng Yang. "Substitution Rates in Drosophila Nuclear Genes: Implications for Translational Selection." Genetics 157, no. 1 (January 1, 2001): 295–305. http://dx.doi.org/10.1093/genetics/157.1.295.
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AbstractThe relationships between synonymous and nonsynonymous substitution rates and between synonymous rate and codon usage bias are important to our understanding of the roles of mutation and selection in the evolution of Drosophila genes. Previous studies used approximate estimation methods that ignore codon bias. In this study we reexamine those relationships using maximum-likelihood methods to estimate substitution rates, which accommodate the transition/transversion rate bias and codon usage bias. We compiled a sample of homologous DNA sequences at 83 nuclear loci from Drosophila melanogaster and at least one other species of Drosophila. Our analysis was consistent with previous studies in finding that synonymous rates were positively correlated with nonsynonymous rates. Our analysis differed from previous studies, however, in that synonymous rates were unrelated to codon bias. We therefore conducted a simulation study to investigate the differences between approaches. The results suggested that failure to properly account for multiple substitutions at the same site and for biased codon usage by approximate methods can lead to an artifactual correlation between synonymous rate and codon bias. Implications of the results for translational selection are discussed.
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Berlin, Sofia, Mikael Brandström, Niclas Backström, Erik Axelsson, Nick G. C. Smith, and Hans Ellegren. "Substitution Rate Heterogeneity and the Male Mutation Bias." Journal of Molecular Evolution 62, no. 2 (February 2006): 226–33. http://dx.doi.org/10.1007/s00239-005-0103-6.
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Duchêne, Sebastián, Edward C. Holmes, and Simon Y. W. Ho. "Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates." Proceedings of the Royal Society B: Biological Sciences 281, no. 1786 (July 7, 2014): 20140732. http://dx.doi.org/10.1098/rspb.2014.0732.
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Time-scales of viral evolution and emergence have been studied widely, but are often poorly understood. Molecular analyses of viral evolutionary time-scales generally rely on estimates of rates of nucleotide substitution, which vary by several orders of magnitude depending on the timeframe of measurement. We analysed data from all major groups of viruses and found a strong negative relationship between estimates of nucleotide substitution rate and evolutionary timescale. Strikingly, this relationship was upheld both within and among diverse groups of viruses. A detailed case study of primate lentiviruses revealed that the combined effects of sequence saturation and purifying selection can explain this time-dependent pattern of rate variation. Therefore, our analyses show that studies of evolutionary time-scales in viruses require a reconsideration of substitution rates as a dynamic, rather than as a static, feature of molecular evolution. Improved modelling of viral evolutionary rates has the potential to change our understanding of virus origins.
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Elango, Navin, Jeeyoung Lee, Zuogang Peng, Yong-Hwee E. Loh, and Soojin V. Yi. "Evolutionary rate variation in Old World monkeys." Biology Letters 5, no. 3 (March 4, 2009): 405–8. http://dx.doi.org/10.1098/rsbl.2008.0712.
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We analysed over 8 million base pairs of bacterial artificial chromosome-based sequence alignments of four Old World monkeys and the human genome. Our findings are as follows. (i) Genomic divergences among several Old World monkeys mirror those between well-studied hominoids. (ii) The X-chromosome evolves slower than autosomes, in accord with ‘male-driven evolution’. However, the degree of male mutation bias is lower in Old World monkeys than in hominoids. (iii) Evolutionary rates vary significantly between lineages. The baboon branch shows a particularly slow molecular evolution. Thus, lineage-specific evolutionary rate variation is a common theme of primate genome evolution. (iv) In contrast to the overall pattern, mutations originating from DNA methylation exhibit little variation between lineages. Our study illustrates the potential of primates as a model system to investigate genome evolution, in particular to elucidate molecular mechanisms of substitution rate variation.
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Stolyarova, Anastasia V., Georgii A. Bazykin, Tatyana V. Neretina, and Alexey S. Kondrashov. "Bursts of amino acid replacements in protein evolution." Royal Society Open Science 6, no. 3 (March 2019): 181095. http://dx.doi.org/10.1098/rsos.181095.
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Evolution can occur both gradually and through alternating episodes of stasis and rapid changes. However, the prevalence and magnitude of fluctuations of the rate of evolution remain obscure. Detecting a rapid burst of changes requires a detailed record of past evolution, so that events that occurred within a short time interval can be identified. Here, we use the phylogenies of the Baikal Lake amphipods and of Catarrhini, which contain very short internal edges which make this task feasible. We detect six salient bursts of evolution of individual proteins during such short time periods, each involving between six and 38 amino acid substitutions. These bursts were extremely unlikely to have occurred neutrally, and were apparently caused by positive selection. On average, in the course of a time interval required for one synonymous substitution per site, a protein undergoes a strong burst of rapid evolution with probability at least approximately 0.01.
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Carulli, J. P., and D. L. Hartl. "Variable rates of evolution among Drosophila opsin genes." Genetics 132, no. 1 (September 1, 1992): 193–204. http://dx.doi.org/10.1093/genetics/132.1.193.
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Abstract DNA sequences and chromosomal locations of four Drosophila pseudoobscura opsin genes were compared with those from Drosophila melanogaster, to determine factors that influence the evolution of multigene families. Although the opsin proteins perform the same primary functions, the comparisons reveal a wide range of evolutionary rates. Amino acid identities for the opsins range from 90% for Rh2 to more than 95% for Rh1 and Rh4. Variation in the rate of synonymous site substitution is especially striking: the major opsin, encoded by the Rh1 locus, differs at only 26.1% of synonymous sites between D. pseudoobscura and D. melanogaster, while the other opsin loci differ by as much as 39.2% at synonymous sites. Rh3 and Rh4 have similar levels of synonymous nucleotide substitution but significantly different amounts of amino acid replacement. This decoupling of nucleotide substitution and amino acid replacement suggests that different selective pressures are acting on these similar genes. There is significant heterogeneity in base composition and codon usage bias among the opsin genes in both species, but there are no consistent relationships between these factors and the rate of evolution of the opsins. In addition to exhibiting variation in evolutionary rates, the opsin loci in these species reveal rearrangements of chromosome elements.
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Pracana, Rodrigo, Adam D. Hargreaves, John F. Mulley, and Peter W. H. Holland. "Runaway GC Evolution in Gerbil Genomes." Molecular Biology and Evolution 37, no. 8 (April 24, 2020): 2197–210. http://dx.doi.org/10.1093/molbev/msaa072.
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Abstract Recombination increases the local GC-content in genomic regions through GC-biased gene conversion (gBGC). The recent discovery of a large genomic region with extreme GC-content in the fat sand rat Psammomys obesus provides a model to study the effects of gBGC on chromosome evolution. Here, we compare the GC-content and GC-to-AT substitution patterns across protein-coding genes of four gerbil species and two murine rodents (mouse and rat). We find that the known high-GC region is present in all the gerbils, and is characterized by high substitution rates for all mutational categories (AT-to-GC, GC-to-AT, and GC-conservative) both at synonymous and nonsynonymous sites. A higher AT-to-GC than GC-to-AT rate is consistent with the high GC-content. Additionally, we find more than 300 genes outside the known region with outlying values of AT-to-GC synonymous substitution rates in gerbils. Of these, over 30% are organized into at least 17 large clusters observable at the megabase-scale. The unusual GC-skewed substitution pattern suggests the evolution of genomic regions with very high recombination rates in the gerbil lineage, which can lead to a runaway increase in GC-content. Our results imply that rapid evolution of GC-content is possible in mammals, with gerbil species providing a powerful model to study the mechanisms of gBGC.
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Ohashi, Jun, and Katsushi Tokunaga. "Sojourn Times and Substitution Rate at Overdominant and Linked Neutral Loci." Genetics 155, no. 2 (June 1, 2000): 921–27. http://dx.doi.org/10.1093/genetics/155.2.921.
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Abstract The sojourn times until fixation of an overdominant allele were investigated based on the diffusion equation. Furthermore, the rate of accumulation of mutations, or the substitution rate, was predicted from the mean extinction time of a common overdominant allele. The substitution rate calculated theoretically agreed well with that determined by computer simulation. Overdominant selection enhances the polymorphism at linked loci, while its effect on the sojourn times and the substitution rate at linked loci has not been studied yet. To solve these problems, a model that assumed two linked loci, each with infinite alleles, was examined by computer simulation. A decrease in the recombination rate between two loci markedly changed the distribution of sojourn times of a neutral allele. Although overdominant selection obviously increased the sojourn times and the polymorphism at a linked locus, the rate of nucleotide substitution at the neutral locus was not influenced significantly even if complete linkage was assumed. These results suggest that, in regions containing overdominant genes, linked neutral loci will exhibit elevated levels of polymorphism, but their rate of molecular evolution remains that predicted by neutral theory.
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Hoenen, T., D. Safronetz, A. Groseth, K. R. Wollenberg, O. A. Koita, B. Diarra, I. S. Fall, et al. "Mutation rate and genotype variation of Ebola virus from Mali case sequences." Science 348, no. 6230 (March 26, 2015): 117–19. http://dx.doi.org/10.1126/science.aaa5646.
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The occurrence of Ebola virus (EBOV) in West Africa during 2013–2015 is unprecedented. Early reports suggested that in this outbreak EBOV is mutating twice as fast as previously observed, which indicates the potential for changes in transmissibility and virulence and could render current molecular diagnostics and countermeasures ineffective. We have determined additional full-length sequences from two clusters of imported EBOV infections into Mali, and we show that the nucleotide substitution rate (1.3 × 10–3 substitutions per site per year) is consistent with rates observed in Central African outbreaks. In addition, overall variation among all genotypes observed remains low. Thus, our data indicate that EBOV is not undergoing rapid evolution in humans during the current outbreak. This finding has important implications for outbreak response and public health decisions and should alleviate several previously raised concerns.
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Linder, Martin, Tom Britton, and Bengt Sennblad. "Evaluation of Bayesian Models of Substitution Rate Evolution—Parental Guidance versus Mutual Independence." Systematic Biology 60, no. 3 (March 8, 2011): 329–42. http://dx.doi.org/10.1093/sysbio/syr009.
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Zhou, Nan, Mingma Li, Yue Huang, Lu Zhou, and Bei Wang. "Genetic Characterizations and Molecular Evolution of the Measles Virus Genotype B3’s Hemagglutinin (H) Gene in the Elimination Era." Viruses 13, no. 10 (September 30, 2021): 1970. http://dx.doi.org/10.3390/v13101970.
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Measles virus (MeV) genotype B3 is one globally significant circulating genotype. Here, we present a systematic description of long-term evolutionary characterizations of the MeV genotype B3’s hemagglutinin (H) gene in the elimination era. Our results show that the B3 H gene can be divided into two main sub-genotypes, and the highest intra-genotypic diversity was observed in 2004. MeV genotype B3’s H gene diverged in 1976; its overall nucleotide substitution rate is estimated to be 5.697 × 10−4 substitutions/site/year, and is slowing down. The amino acid substitution rate of genotype B3’s H gene is also decreasing, and the mean effective population size has been in a downward trend since 2000. Selection pressure analysis only recognized a few sites under positive selection, and the number of positive selection sites is getting smaller. All of these observations may reveal that genotype B3’s H gene is not under strong selection pressure, and is becoming increasingly conservative. MeV H-gene or whole-genome sequencing should be routine, so as to better elucidate the molecular epidemiology of MeV in the future.
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Jiménez-Santos, María José, Miguel Arenas, and Ugo Bastolla. "Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution." PeerJ 6 (October 5, 2018): e5549. http://dx.doi.org/10.7717/peerj.5549.
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The number of amino acids that occupy a given protein site during evolution reflects the selective constraints operating on the site. This evolutionary variability is strongly influenced by the structural properties of the site in the native structure, and it is quantified either through sequence entropy or through substitution rates. However, while the sequence entropy only depends on the equilibrium frequencies of the amino acids, the substitution rate also depends on the exchangeability matrix that describes mutations in the mathematical model of the substitution process. Here we apply two variants of a mathematical model of protein evolution with selection for protein stability, both against unfolding and against misfolding. Exploiting the approximation of independent sites, these models allow computing site-specific substitution processes that satisfy global constraints on folding stability. We find that site-specific substitution rates do not depend only on the selective constraints acting on the site, quantified through its sequence entropy. In fact, polar sites evolve faster than hydrophobic sites even for equal sequence entropy, as a consequence of the fact that polar amino acids are characterized by higher mutational exchangeability than hydrophobic ones. Accordingly, the model predicts that more polar proteins tend to evolve faster. Nevertheless, these results change if we compare proteins that evolve under different mutation biases, such as orthologous proteins in different bacterial genomes. In this case, the substitution rates are faster in genomes that evolve under mutational bias that favor hydrophobic amino acids by preferentially incorporating the nucleotide Thymine that is more frequent in hydrophobic codons. This appearingly contradictory result arises because buried sites occupied by hydrophobic amino acids are characterized by larger selective factors that largely amplify the substitution rate between hydrophobic amino acids, while the selective factors of exposed sites have a weaker effect. Thus, changes in the mutational bias produce deep effects on the biophysical properties of the protein (hydrophobicity) and on its evolutionary properties (sequence entropy and substitution rate) at the same time. The program Prot_evol that implements the two site-specific substitution processes is freely available at https://ub.cbm.uam.es/prot_fold_evol/prot_fold_evol_soft_main.php#Prot_Evol.
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Vijg, Jan, Xiao Dong, Brandon Milholland, and Lei Zhang. "Genome instability: a conserved mechanism of ageing?" Essays in Biochemistry 61, no. 3 (May 26, 2017): 305–15. http://dx.doi.org/10.1042/ebc20160082.
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DNA is the carrier of genetic information and the primary template from which all cellular information is ultimately derived. Changes in the DNA information content through mutation generate diversity for evolution through natural selection but are also a source of deleterious effects. It has since long been hypothesized that mutation accumulation in somatic cells of multicellular organisms could causally contribute to age-related cellular degeneration and death. Assays to detect different types of mutations, from base substitutions to large chromosomal aberrations, have been developed and show unequivocally that mutations accumulate in different tissues and cell types of ageing humans and animals. More recently, next-generation sequencing-based methods have been developed to accurately determine the complete landscape of base substitution mutations in single cells. The first results show that the somatic mutation rate is much higher than the germline mutation rate and that base substitution loads in somatic cells are high enough to potentially affect cellular function.
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Wolstenholme, David R., and Douglas O. Clary. "SEQUENCE EVOLUTION OF DROSOPHILA MITOCHONDRIAL DNA." Genetics 109, no. 4 (April 1, 1985): 725–44. http://dx.doi.org/10.1093/genetics/109.4.725.
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ABSTRACT We have compared nucleotide sequences of corresponding segments of the mitochondrial DNA (mtDNA) molecules of Drosophila yakuba and Drosophila melanogaster, which contain the genes for six proteins and seven tRNAs. The overall frequency of substitution between the nucleotide sequences of these protein genes is 7.2%. As was found for mtDNAs from closely related mammals, most substitutions (86%) in Drosophila mitochondrial protein genes do not result in an amino acid replacement. However, the frequencies of transitions and transversions are approximately equal in Drosophila mtDNAs, which is in contrast to the vast excess of transitions over transversions in mammalian mtDNAs. In Drosophila mtDNAs the frequency of C ↔ T substitutions per codon in the third position is 2.5 times greater among codons of two-codon families than among codons of four-codon families; this is contrary to the hypothesis that third position silent substitutions are neutral in regard to selection. In the third position of codons of four-codon families transversions are 4.6 times more frequent than transitions and A ↔ T substitutions account for 86% of all transversions. Ninety-four percent of all codons in the Drosophila mtDNA segments analyzed end in A or T. However, as this alone cannot account for the observed high frequency of A ↔ T substitutions there must be either a disproportionately high rate of A ↔ T mutation in Drosophila mtDNA or selection bias for the products of A ↔ T mutation.—Consideration of the frequencies of interchange of AGA and AGT codons in the corresponding D. yakuba and D. melanogaster mitochondrial protein genes provides strong support for the view that AGA specifies serine in the Drosophila mitochondrial genetic code.