Academic literature on the topic 'Substitution rate evolution'
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Journal articles on the topic "Substitution rate evolution"
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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.
Full textDissertations / Theses on the topic "Substitution rate evolution"
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Botha, Stephen Gordon. "The effect of evolutionary rate estimation methods on correlations observed between substitution rates in models of evolution." Thesis, Stellenbosch : Stellenbosch University, 2012. http://hdl.handle.net/10019.1/19938.
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Mugal, Carina Farah. "Nucleotide Substitution Patterns in Vertebrate Genomes." Doctoral thesis, Uppsala universitet, Evolutionsbiologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-198787.
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The rates and patterns at which nucleotide substitutions occur vary significantly across the genome sequence of vertebrates. A prominent example is the difference in the rate of evolution of functional sequences versus nonfunctional (neutrally evolving) sequences, which is explained by the influence of natural selection on functional sequences. However, even within neutrally evolving sequences there is striking variation in the rates and patterns of nucleotide substitutions. Unraveling the underlying processes that induce this variation is necessary to understand the basic principles of variation in neutral substitution profiles, which in turn is crucial for the identification of regions in the genome where natural selection acts. This research question builds the main focus of the present thesis. I have studied the causes and consequences of variation in different patterns of nucleotide substitutions. In particular, I have investigated substitutional strand asymmetries in mammalian genes and could show that they result from the asymmetric nature of DNA replication and transcription. Comparative analysis of substitutional asymmetries then suggested that the organization of DNA replication and the level of transcription are conserved among mammals. Further, I have examined the variation in CpG mutation rate among human genes and could show that beside DNA methylation also GC content plays a decisive role in CpG mutability. In addition, I have studied the signatures of GC-biased gene conversion and its impact on the evolution of the GC isochore structure in chicken. By comparison of the results in chicken to previous results in human I found evidence that karyotype stability is critical for the evolution of GC isochores. Finally, beside the empirical studies, I have performed theoretical investigations of substitution rates in functional sequences. More precisely, I have explored the temporal dynamics of estimates of the ratio of non-synonymous to synonymous substitution rates dN/dS in a phylogentic-population genetic framework.
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Raj, Kumar Praveen Kumar. "APPLICATION OF TRANSCRIPTOMICS TO ADDRESS QUESTIONS IN MOLECULAR BIOLOGY AND EVOLUTION." Miami University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=miami1410427259.
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Hermansen, Russell A., Brian K. Mannakee, Wolfgang Knecht, David A. Liberles, and Ryan N. Gutenkunst. "Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast." BioMed Central Ltd, 2015. http://hdl.handle.net/10150/610280.
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BACKGROUND: Selection on proteins is typically measured with the assumption that each protein acts independently. However, selection more likely acts at higher levels of biological organization, requiring an integrative view of protein function. Here, we built a kinetic model for de novo pyrimidine biosynthesis in the yeast Saccharomyces cerevisiae to relate pathway function to selective pressures on individual protein-encoding genes. RESULTS: Gene families across yeast were constructed for each member of the pathway and the ratio of nonsynonymous to synonymous nucleotide substitution rates (dN/dS) was estimated for each enzyme from S. cerevisiae and closely related species. We found a positive relationship between the influence that each enzyme has on pathway function and its selective constraint. CONCLUSIONS: We expect this trend to be locally present for enzymes that have pathway control, but over longer evolutionary timescales we expect that mutation-selection balance may change the enzymes that have pathway control.
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Berlin, Sofia. "The Effects of Mutation and Selection on the Rate and Pattern of Molecular Evolution in Birds." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4516.
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Jung, Matthieu. "Evolution du VIH : méthodes, modèles et algorithmes." Thesis, Montpellier 2, 2012. http://www.theses.fr/2012MON20052/document.
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La donnée de séquences nucléotidiques permet d'inférer des arbres phylogénétiques, ou phylogénies, qui décrivent leur lien de parenté au cours de l'évolution. Associer à ces séquences leur date de prélèvement ou leur pays de collecte, permet d'inférer la localisation temporelle ou spatiale de leurs ancêtres communs. Ces données et procédures sont très utilisées pour les séquences de virus et, notamment, celles du virus de l'immunodéficience humaine (VIH), afin d'en retracer l'histoire épidémique à la surface du globe et au cours du temps. L'utilisation de séquences échantillonnées à des moments différents (ou hétérochrones) sert aussi à estimer leur taux de substitution, qui caractérise la vitesse à laquelle elles évoluent.Les méthodes les plus couramment utilisées pour ces différentes tâches sont précises, mais lourdes en temps de calcul car basées sur des modèles complexes, et ne peuvent traiter que quelques centaines de séquences. Devant le nombre croissant de séquences disponibles dans les bases de données, souvent plusieurs milliers pour une étude donnée, le développement de méthodes rapides et efficaces devient indispensable. Nous présentons une méthode de distances, Ultrametric Least Squares, basée sur le principe des moindres carrés, souvent utilisé en phylogénie, qui permet d'estimer le taux de substitution d'un ensemble de séquences hétérochrones, dont on déduit ensuite facilement les dates des spéciations ancestrales. Nous montrons que le critère à optimiser est parabolique par morceaux et proposons un algorithme efficace pour trouver l'optimum global.L'utilisation de séquences échantillonnées en des lieux différents permet aussi de retracer les chaînes de transmission d'une épidémie. Dans ce cadre, nous utilisons la totalité des séquences disponibles (~3 500) du sous-type C du VIH-1 (VIH de type 1), responsable de près de 50% des infections mondiales au VIH-1, pour estimer ses principaux flux migratoires à l'échelle mondiale, ainsi que son origine géographique. Des outils novateurs, basés sur le principe de parcimonie combiné avec différents critères statistiques, sont utilisés afin de synthétiser et interpréter l'information contenue dans une grande phylogénie représentant l'ensemble des séquences étudiées. Enfin, l'origine géographique et temporelle de ce variant (VIH-1 C) au Sénégal est précisément explorée lors d'une seconde étude, portant notamment sur les hommes ayant des rapports sexuels avec des hommesNucleotide sequences data enable the inference of phylogenetic trees, or phylogenies, describing their evolutionary re-lationships during evolution. Combining these sequences with their sampling date or country of origin, allows inferring the temporal or spatial localization of their common ancestors. These data and methods are widely used with viral sequences, and particularly with human immunodeficiency virus (HIV), to trace the viral epidemic history over time and throughout the globe. Using sequences sampled at different points in time (or heterochronous) is also a mean to estimate their substitution rate, which characterizes the speed of evolution. The most commonly used methods to achieve these tasks are accurate, but are computationally heavy since they are based on complex models, and can only handle few hundreds of sequences. With an increasing number of sequences avail-able in the databases, often several thousand for a given study, the development of fast and accurate methods becomes essential. Here, we present a new distance-based method, named Ultrametric Least Squares, which is based on the princi-ple of least squares (very popular in phylogenetics) to estimate the substitution rate of a set of heterochronous sequences and the dates of their most recent common ancestors. We demonstrate that the criterion to be optimized is piecewise parabolic, and provide an efficient algorithm to find the global minimum.Using sequences sampled at different locations also helps to trace transmission chains of an epidemic. In this respect, we used all available sequences (~3,500) of HIV-1 subtype C, responsible for nearly 50% of global HIV-1 infections, to estimate its major migratory flows on a worldwide scale and its geographic origin. Innovative tools, based on the principle of parsimony, combined with several statistical criteria were used to synthesize and interpret information in a large phylogeny representing all the studied sequences. Finally, the temporal and geographical origins of the HIV-1 subtype C in Senegal were further explored and more specifically for men who have sex with men
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Axelsson, Erik. "Comparative Genomics in Birds." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7432.
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Saclier, Nathanaëlle. "Origine des variations de taux d’évolution moléculaire inter-spécifiques : apport d’un modèle génomique en milieu souterrain." Thesis, Lyon, 2019. https://n2t.net/ark:/47881/m69p310z.
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La vitesse à laquelle les séquences d’ADN évoluent varie selon les espèces. Ces différences peuvent venir de caractéristiques intrinsèques de l’espèce (taux métabolique, traits d’histoire de vie) ou de son environnement (rayonnements ionisants). L’objectif de cette thèse est de tester les principales hypothèses expliquant les variations de taux d’évolution moléculaire entre les espèces. Pour cela, les particularités des Asellidae souterrains ont été couplées avec des données de séquençage nouvelle génération dans le génome nucléaire et le génome mitochondrial. L’utilisation des Asellidae comme modèle biologique nous permet d’avoir, au sein du même groupe, des espèces ayant indépendamment effectuées une transition vers le milieu souterrain. Cette transition étant accompagnée de nombreux changements, tant biologiques (longévité, taux métabolique, temps de génération) qu’environnementaux, elle nous permet, au sein du même groupe, de pouvoir comparer des espèces contrastées en termes de longévité, de taille de populations, de rayonnements ionisants ou encore de productivité et de température. De plus, parce que ces organismes dispersent peu, ils persistent dans le même environnement durant de nombreuses générations, permettant de préciser et de quantifier les facteurs responsables de variations du taux d’évolution moléculaire entre les espèces.Cette approche nous a permis de mettre en évidence un effet du temps de génération sur le taux d’évolution du génome nucléaire mais pas sur le génome mitochondrial. Un effet de la radioactivité naturelle, d’une ampleur analogue à celle du temps de génération a également été mis en évidence. Enfin, l’étude des variations des taux d’évolution moléculaire à une échelle globale a révélée des biais dans les calculs des taux de substitutions qui devront être pris en compte dans les études cherchant a établir le lien entre le taux de mutations et la diversificationThe rate at which DNA accumulates substitutions varies widely among species. Rate variations have been imputed to species intrinsic features (metabolic rate, life history traits) or to the environment characteristics (ionizing radiations, selection pressure). The aim of this PhD project was to investigate the main hypotheses explaining variations in the rate of molecular evolution between species. To achieve that, we combined the unique properties of subterranean isopods from the Asellidae family and high-throughput sequencing data from the nuclear and mitochondrial genome. Asellidae species have made multiple independent transitions to subterranean environments where subterranean species have repeatedly evolved a lower metabolic rate, a longer lifespan and a longer generation time. Moreover, because they are poor dispersers, they are exposed to the same environment across many generations, allowing us to compare species with long-term contrasted features in term of life history traits and environmental characteristics. We found that generation time negatively impact the rate of molecular evolution in the nuclear genome whereas the mitochondrial rate remained unchanged. We also found an increase of the mutation rate for species living in naturally highly radioactive environments. Finally, the study of the rate of molecular evolution variation at a global scale brought forward a systematic bias which needs to be taken into account in studying the link between the mutation rate and diversification
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Erixon, Per. "Phylogenetic Support and Chloroplast Genome Evolution in Sileneae (Caryophyllaceae)." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Universitetsbiblioteket [distributör], 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7166.
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Künstner, Axel. "Birds as a Model for Comparative Genomic Studies." Doctoral thesis, Uppsala universitet, Evolutionsbiologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-159766.
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Comparative genomics provides a tool to investigate large biological datasets, i.e. genomic datasets. In my thesis I focused on inferring patterns of selection in coding and non-coding regions of avian genomes. Until recently, large comparative studies on selection were mainly restricted to model species with sequenced genomes. This limitation has been overcome with advances in sequencing technologies and it is now possible to gather large genomic data sets for non-model species. Next-generation sequencing data was used to study patterns of nucleotide substitutions and from this we inferred how selection has acted in the genomes of 10 non-model bird species. In general, we found evidence for a negative correlation between neutral substitution rate and chromosome size in birds. In a follow up study, we investigated two closely related bird species, to study expression levels in different tissues and pattern of selection. We found that between 2% and 18% of all genes were differentially expressed between the two species. We showed that non-coding regions adjacent to genes are under evolutionary constraint in birds, which suggests that noncoding DNA plays an important functional role in the genome. Regions downstream to genes (3’) showed particularly high level of constraint. The level of constraint in these regions was not correlated to the length of untranslated regions, which suggests that other causes play also a role in sequence conservation. We compared the rate of nonsynonymous substitutions to the rate of synonymous substitutions in order to infer levels of selection in protein-coding sequences. Synonymous substitutions are often assumed to evolve neutrally. We studied synonymous substitutions by estimating constraint on 4-fold degenerate sites of avian genes and found significant evolutionary constraint on this category of sites (between 24% and 43%). These results call for a reappraisal of synonymous substitution rates being used as neutral standards in molecular evolutionary analysis (e.g. the dN/dS ratio to infer positive selection). Finally, the problem of sequencing errors in next-generation sequencing data was investigated. We developed a program that removes erroneous bases from the reads. We showed that low coverage sequencing projects and large genome sequencing projects will especially gain from trimming erroneous reads.
Books on the topic "Substitution rate evolution"
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Renner, Tanya, Tianying Lan, Kimberly M. Farr, Enrique Ibarra-Laclette, Luis Herrera-Estrella, Stephan C. Schuster, Mitsuyasu Hasebe, Kenji Fukushima, and Victor A. Albert. Carnivorous plant genomes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198779841.003.0011.
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Carnivorous plant genome research has focused on members of the Lamiales and Oxalidales; the most complete sequences are for Utricularia gibba and Cephalotus follicularis. The size-limited U. gibba genome highlights the importance of small-scale tandem duplications, which likely play roles in this species’ carnivorous adaptation. Sequencing of the C. follicularis genome detected adaptive changes that may explain the evolution of traits associated with attraction, trapping, digestion, and absorption. Functional consequences of genes putatively missing in the U. gibba genome, yet present in other angiosperms, may have influenced the evolution of polyploidy, physiology, and a rootless Bauplan. Additional draft nuclear genomes and transcriptomes are available for carnivorous Caryophyllales, Ericales, Lamiales, and Poales, but are limited in quantity and quality. Chloroplast genomes of carnivorous Lentibulariaceae have revealed interesting patterns of gene loss, alterations in the proportion of repeat DNA, and plastome-wide increases in substitution rates.
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Pamuk, Sevket. Uneven Centuries. Princeton University Press, 2018. http://dx.doi.org/10.23943/princeton/9780691166377.001.0001.
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The population and economy of the area within the present-day borders of Turkey has consistently been among the largest in the developing world, yet there has been no authoritative economic history of Turkey until now. This book examines the economic growth and human development of Turkey over the past two hundred years. Taking a comparative global perspective, the book investigates Turkey's economic history through four periods: the open economy during the nineteenth-century Ottoman era, the transition from empire to nation-state that spanned the two world wars and the Great Depression, the continued protectionism and import-substituting industrialization after World War II, and the neoliberal policies and the opening of the economy after 1980. Making use of indices of GDP per capita, trade, wages, health, and education, the book argues that Turkey's long-term economic trends cannot be explained only by immediate causes such as economic policies, rates of investment, productivity growth, and structural change. The book offers a deeper analysis of the essential forces underlying Turkey's development—its institutions and their evolution—to make better sense of the country's unique history and to provide important insights into the patterns of growth in developing countries during the past two centuries.
Book chapters on the topic "Substitution rate evolution"
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Hu, Ting, and Wolfgang Banzhaf. "Nonsynonymous to Synonymous Substitution Ratio $k_{\mathrm a}/k_{\mathrm s}$ : Measurement for Rate of Evolution in Evolutionary Computation." In Parallel Problem Solving from Nature – PPSN X, 448–57. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-87700-4_45.
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Muse, Spencer V. "Examining rates and patterns of nucleotide substitution in plants." In Plant Molecular Evolution, 25–43. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4221-2_2.
Full textConference papers on the topic "Substitution rate evolution"
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Hu, Ting, and Wolfgang Banzhaf. "Measuring rate of evolution in genetic programming using amino acid to synonymous substitution ratioka/ks." In the 10th annual conference. New York, New York, USA: ACM Press, 2008. http://dx.doi.org/10.1145/1389095.1389352.
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Aniello, Andrea, Lorenzo Bartolucci, Stefano Cordiner, Vincenzo Mulone, Sundar R. Krishnan, and Kalyan K. Srinivasan. "CFD Analysis of Diesel-Methane Dual Fuel Low Temperature Combustion at Low Load and High Methane Substitution." In ASME 2018 Internal Combustion Engine Division Fall Technical Conference. American Society of Mechanical Engineers, 2018. http://dx.doi.org/10.1115/icef2018-9649.
Full textAbstract:
Over the last few decades, emissions regulations for internal combustion engines have become increasingly restrictive, pushing researchers around the world to exploit innovative propulsion solutions. Among them, the dual fuel low temperature combustion (LTC) strategy has proven capable of reducing fuel consumption and while meeting emissions regulations for oxides of nitrogen (NOx) and particulate matter (PM) without problematic aftertreatment systems. However, further investigations are still needed to reduce engine-out hydrocarbon (HC) and carbon monoxide (CO) emissions as well as to extend the operational range and to further improve the performance and efficiency of dual-fuel engines. In this scenario, the present study focuses on numerical simulation of fumigated methane-diesel dual fuel LTC in a single-cylinder research engine (SCRE) operating at low load and high methane percent energy substitution (PES). Results are validated against experimental cylinder pressure and apparent heat release rate (AHRR) data. A 3D full-cylinder RANS simulation is used to thoroughly understand the influence of the start of injection (SOI) of diesel fuel on the overall combustion behavior, clarifying the causes of AHRR transition from two-stage AHRR at late SOIs to single-stage AHRR at early SOIs, low temperature heat release (LTHR) behavior, as well as high HC production. The numerical campaign shows that it is crucial to reliably represent the interaction between the diesel spray and the in-cylinder charge to match both local and overall methane energy fraction, which in turn, ensures a proper representation of the whole combustion. To that aim, even a slight deviation (∼3%) of the trapped mass or of the thermodynamic conditions would compromise the numerical accuracy, highlighting the importance of properly capturing all the phenomena occurring during the engine cycle. The comparison between numerical and experimental AHRR curves shows the capability of the numerical framework proposed to correctly represent the dual-fuel combustion process, including low temperature heat release (LTHR) and the transition from two-stage to single stage AHRR with advancing SOI. The numerical simulations allow for quantitative evaluation of the residence time of vapor-phase diesel fuel inside the combustion chamber and at the same time tracking the evolution of local diesel mass fraction during ignition delay — showing their influence on the LTHR phenomena. Oxidation regions of diesel and ignition points of methane are also displayed for each case, clarifying the reasons for the observed differences in combustion evolution at different SOIs.