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Journal articles on the topic 'Mutation rate evolution'

Author: Grafiati

Published: 22 June 2024

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1

Trindade, Sandra, Lilia Perfeito, and Isabel Gordo. "Rate and effects of spontaneous mutations that affect fitness in mutator Escherichia coli." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1544 (2010): 1177–86. http://dx.doi.org/10.1098/rstb.2009.0287.

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Knowledge of the mutational parameters that affect the evolution of organisms is of key importance in understanding the evolution of several characteristics of many natural populations, including recombination and mutation rates. In this study, we estimated the rate and mean effect of spontaneous mutations that affect fitness in a mutator strain of Escherichia coli and review some of the estimation methods associated with mutation accumulation (MA) experiments. We performed an MA experiment where we followed the evolution of 50 independent mutator lines that were subjected to repeated bottlene

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Sherer, Nicholas A., and Thomas E. Kuhlman. "Escherichia coli with a Tunable Point Mutation Rate for Evolution Experiments." G3: Genes|Genomes|Genetics 10, no. 8 (2020): 2671–81. http://dx.doi.org/10.1534/g3.120.401124.

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The mutation rate and mutations’ effects on fitness are crucial to evolution. Mutation rates are under selection due to linkage between mutation rate modifiers and mutations’ effects on fitness. The linkage between a higher mutation rate and more beneficial mutations selects for higher mutation rates, while the linkage between a higher mutation rate and more deleterious mutations selects for lower mutation rates. The net direction of selection on mutations rates depends on the fitness landscape, and a great deal of work has elucidated the fitness landscapes of mutations. However, tests of the

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3

Stephan, Wolfgang. "The Rate of Compensatory Evolution." Genetics 144, no. 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 in

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4

Sniegowski, Paul. "Evolution: Setting the mutation rate." Current Biology 7, no. 8 (1997): R487—R488. http://dx.doi.org/10.1016/s0960-9822(06)00244-2.

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5

Lynch, Michael. "Evolution of the mutation rate." Trends in Genetics 26, no. 8 (2010): 345–52. http://dx.doi.org/10.1016/j.tig.2010.05.003.

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Schoen, Daniel J., and Stewart T. Schultz. "Somatic Mutation and Evolution in Plants." Annual Review of Ecology, Evolution, and Systematics 50, no. 1 (2019): 49–73. http://dx.doi.org/10.1146/annurev-ecolsys-110218-024955.

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Somatic mutations are common in plants, and they may accumulate and be passed on to gametes. The determinants of somatic mutation accumulation include the intraorganismal selective effect of mutations, the number of cell divisions that separate the zygote from the formation of gametes, and shoot apical meristem structure and branching. Somatic mutations can promote the evolution of diploidy, polyploidy, sexual recombination, outcrossing, clonality, and separate sexes, and they may contribute genetic variability in many other traits. The amplification of beneficial mutations via intraorganismal

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Krasovec, Marc, Rosalind E. M. Rickaby, and Dmitry A. Filatov. "Evolution of Mutation Rate in Astronomically Large Phytoplankton Populations." Genome Biology and Evolution 12, no. 7 (2020): 1051–59. http://dx.doi.org/10.1093/gbe/evaa131.

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Abstract Genetic diversity is expected to be proportional to population size, yet, there is a well-known, but unexplained lack of genetic diversity in large populations—the “Lewontin’s paradox.” Larger populations are expected to evolve lower mutation rates, which may help to explain this paradox. Here, we test this conjecture by measuring the spontaneous mutation rate in a ubiquitous unicellular marine phytoplankton species Emiliania huxleyi (Haptophyta) that has modest genetic diversity despite an astronomically large population size. Genome sequencing of E. huxleyi mutation accumulation lin

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Edlund, Jeffrey A., and Christoph Adami. "Evolution of Robustness in Digital Organisms." Artificial Life 10, no. 2 (2004): 167–79. http://dx.doi.org/10.1162/106454604773563595.

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We study the evolution of robustness in digital organisms adapting to a high mutation rate. As genomes adjust to the harsh mutational environment, the mean effect of single mutations decreases, up until the point where a sizable fraction (up to 30% in many cases) of the mutations are neutral. We correlate the changes in robustness along the line of descent to changes in directional epistasis, and find that increased robustness is achieved by moving from antagonistic epistasis between mutations towards codes where mutations are, on average, independent. We interpret this recoding as a breakup o

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Komp Lindgren, Patricia, Åsa Karlsson, and Diarmaid Hughes. "Mutation Rate and Evolution of Fluoroquinolone Resistance in Escherichia coli Isolates from Patients with Urinary Tract Infections." Antimicrobial Agents and Chemotherapy 47, no. 10 (2003): 3222–32. http://dx.doi.org/10.1128/aac.47.10.3222-3232.2003.

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ABSTRACT Escherichia coli strains from patients with uncomplicated urinary tract infections were examined by DNA sequencing for fluoroquinolone resistance-associated mutations in six genes: gyrA, gyrB, parC, parE, marOR, and acrR. The 54 strains analyzed had a susceptibility range distributed across 15 dilutions of the fluoroquinolone MICs. There was a correlation between the fluoroquinolone MIC and the number of resistance mutations that a strain carried, with resistant strains having mutations in two to five of these genes. Most resistant strains carried two mutations in gyrA and one mutatio

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Gerrish, Philip J., Alexandre Colato, and Paul D. Sniegowski. "Genomic mutation rates that neutralize adaptive evolution and natural selection." Journal of The Royal Society Interface 10, no. 85 (2013): 20130329. http://dx.doi.org/10.1098/rsif.2013.0329.

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When mutation rates are low, natural selection remains effective, and increasing the mutation rate can give rise to an increase in adaptation rate. When mutation rates are high to begin with, however, increasing the mutation rate may have a detrimental effect because of the overwhelming presence of deleterious mutations. Indeed, if mutation rates are high enough: (i) adaptive evolution may be neutralized, resulting in a zero (or negative) adaptation rate despite the continued availability of adaptive and/or compensatory mutations, or (ii) natural selection may be neutralized, because the fitne

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Kondrashov, Alexey S. "Modifiers of mutation-selection balance: general approach and the evolution of mutation rates." Genetical Research 66, no. 1 (1995): 53–69. http://dx.doi.org/10.1017/s001667230003439x.

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SummaryA general approach is developed to estimate secondary selection at a modifier locus that influences some feature of a population under mutation-selection balance. The approach is based on the assumption that the properties of all available genotypes at this locus are similar. Then mutation-selection balance and weak associations between genotype distributions at selectable loci and the modifier locus are established rapidly. In contrast, changes of frequencies of the modifier genotypes are slow, and lead to only slow and small changes of the other features of the population. Thus, while

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12

Johnson, Toby. "Beneficial Mutations, Hitchhiking and the Evolution of Mutation Rates in Sexual Populations." Genetics 151, no. 4 (1999): 1621–31. http://dx.doi.org/10.1093/genetics/151.4.1621.

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Abstract Natural selection acts in three ways on heritable variation for mutation rates. A modifier allele that increases the mutation rate is (i) disfavored due to association with deleterious mutations, but is also favored due to (ii) association with beneficial mutations and (iii) the reduced costs of lower fidelity replication. When a unique beneficial mutation arises and sweeps to fixation, genetic hitchhiking may cause a substantial change in the frequency of a modifier of mutation rate. In previous studies of the evolution of mutation rates in sexual populations, this effect has been un

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Barton, N. H. "Mutation and the evolution of recombination." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1544 (2010): 1281–94. http://dx.doi.org/10.1098/rstb.2009.0320.

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Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill–Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U . This may be large enough to explain high recombi

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Singh, Tanya, Meredith Hyun, and Paul Sniegowski. "Evolution of mutation rates in hypermutable populations of Escherichia coli propagated at very small effective population size." Biology Letters 13, no. 3 (2017): 20160849. http://dx.doi.org/10.1098/rsbl.2016.0849.

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Mutation is the ultimate source of the genetic variation—including variation for mutation rate itself—that fuels evolution. Natural selection can raise or lower the genomic mutation rate of a population by changing the frequencies of mutation rate modifier alleles associated with beneficial and deleterious mutations. Existing theory and observations suggest that where selection is minimized, rapid systematic evolution of mutation rate either up or down is unlikely. Here, we report systematic evolution of higher and lower mutation rates in replicate hypermutable Escherichia coli populations exp

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Nachman, Michael W., and Susan L. Crowell. "Estimate of the Mutation Rate per Nucleotide in Humans." Genetics 156, no. 1 (2000): 297–304. http://dx.doi.org/10.1093/genetics/156.1.297.

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Abstract Many previous estimates of the mutation rate in humans have relied on screens of visible mutants. We investigated the rate and pattern of mutations at the nucleotide level by comparing pseudogenes in humans and chimpanzees to (i) provide an estimate of the average mutation rate per nucleotide, (ii) assess heterogeneity of mutation rate at different sites and for different types of mutations, (iii) test the hypothesis that the X chromosome has a lower mutation rate than autosomes, and (iv) estimate the deleterious mutation rate. Eighteen processed pseudogenes were sequenced, including

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Pfenninger, Markus, Halina Binde Doria, Jana Nickel, Anne Thielsch, Klaus Schwenk, and Mathilde Cordellier. "Spontaneous rate of clonal single nucleotide mutations in Daphnia galeata." PLOS ONE 17, no. 4 (2022): e0265632. http://dx.doi.org/10.1371/journal.pone.0265632.

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Mutations are the ultimate source of heritable variation and therefore the fuel for evolution, but direct estimates of mutation rates exist only for few species. We estimated the spontaneous single nucleotide mutation rate among clonal generations in the waterflea Daphnia galeata with a short-term mutation accumulation approach. Individuals from eighteen mutation accumulation lines over five generations were deep sequenced to count de novo mutations that were not present in a pool of F1 individuals, representing the parental genotype. We identified 12 new nucleotide mutations in 90 clonal gene

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Eskier, Doğa, Gökhan Karakülah, Aslı Suner, and Yavuz Oktay. "RdRp mutations are associated with SARS-CoV-2 genome evolution." PeerJ 8 (July 21, 2020): e9587. http://dx.doi.org/10.7717/peerj.9587.

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COVID-19, caused by the novel SARS-CoV-2 virus, started in China in late 2019, and soon became a global pandemic. With the help of thousands of viral genome sequences that have been accumulating, it has become possible to track the evolution of the viral genome over time as it spread across the world. An important question that still needs to be answered is whether any of the common mutations affect the viral properties, and therefore the disease characteristics. Therefore, we sought to understand the effects of mutations in RNA-dependent RNA polymerase (RdRp), particularly the common 14408C&g

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Sung, W., M. S. Ackerman, S. F. Miller, T. G. Doak, and M. Lynch. "Drift-barrier hypothesis and mutation-rate evolution." Proceedings of the National Academy of Sciences 109, no. 45 (2012): 18488–92. http://dx.doi.org/10.1073/pnas.1216223109.

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Chintalapati, Manjusha, and Priya Moorjani. "Evolution of the mutation rate across primates." Current Opinion in Genetics & Development 62 (June 2020): 58–64. http://dx.doi.org/10.1016/j.gde.2020.05.028.

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Krasovec, Marc, Sophie Sanchez-Brosseau, and Gwenael Piganeau. "First Estimation of the Spontaneous Mutation Rate in Diatoms." Genome Biology and Evolution 11, no. 7 (2019): 1829–37. http://dx.doi.org/10.1093/gbe/evz130.

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Abstract Mutations are the origin of genetic diversity, and the mutation rate is a fundamental parameter to understand all aspects of molecular evolution. The combination of mutation–accumulation experiments and high-throughput sequencing enabled the estimation of mutation rates in most model organisms, but several major eukaryotic lineages remain unexplored. Here, we report the first estimation of the spontaneous mutation rate in a model unicellular eukaryote from the Stramenopile kingdom, the diatom Phaeodactylum tricornutum (strain RCC2967). We sequenced 36 mutation accumulation lines for a

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López-Cortegano, Eugenio, Rory J. Craig, Jobran Chebib, et al. "De Novo Mutation Rate Variation and Its Determinants in Chlamydomonas." Molecular Biology and Evolution 38, no. 9 (2021): 3709–23. http://dx.doi.org/10.1093/molbev/msab140.

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Abstract De novo mutations are central for evolution, since they provide the raw material for natural selection by regenerating genetic variation. However, studying de novo mutations is challenging and is generally restricted to model species, so we have a limited understanding of the evolution of the mutation rate and spectrum between closely related species. Here, we present a mutation accumulation (MA) experiment to study de novo mutation in the unicellular green alga Chlamydomonas incerta and perform comparative analyses with its closest known relative, Chlamydomonas reinhardtii. Using who

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Mawaribuchi, Shuuji, Michihiko Ito, Mitsuaki Ogata, et al. "Meiotic recombination counteracts male-biased mutation (male-driven evolution)." Proceedings of the Royal Society B: Biological Sciences 283, no. 1823 (2016): 20152691. http://dx.doi.org/10.1098/rspb.2015.2691.

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Meiotic recombination is believed to produce greater genetic variation despite the fact that deoxyribonucleic acid (DNA)-replication errors are a major source of mutations. In some vertebrates, mutation rates are higher in males than in females, which developed the theory of male-driven evolution (male-biased mutation). However, there is little molecular evidence regarding the relationships between meiotic recombination and male-biased mutation. Here we tested the theory using the frog Rana rugosa, which has both XX/XY- and ZZ/ZW-type sex-determining systems within the species. The male-to-fem

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Boyce, Kylie J. "Mutators Enhance Adaptive Micro-Evolution in Pathogenic Microbes." Microorganisms 10, no. 2 (2022): 442. http://dx.doi.org/10.3390/microorganisms10020442.

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Adaptation to the changing environmental conditions experienced within a host requires genetic diversity within a microbial population. Genetic diversity arises from mutations which occur due to DNA damage from exposure to exogenous environmental stresses or generated endogenously through respiration or DNA replication errors. As mutations can be deleterious, a delicate balance must be obtained between generating enough mutations for micro-evolution to occur while maintaining fitness and genomic integrity. Pathogenic microorganisms can actively modify their mutation rate to enhance adaptive mi

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Furió, Victoria, Andrés Moya, and Rafael Sanjuán. "The cost of replication fidelity in human immunodeficiency virus type 1." Proceedings of the Royal Society B: Biological Sciences 274, no. 1607 (2006): 225–30. http://dx.doi.org/10.1098/rspb.2006.3732.

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Mutation rates should be governed by at least three evolutionary factors: the need for beneficial mutations, the benefit of minimizing the mutational load and the cost of replication fidelity. RNA viruses show high mutation rates compared with DNA micro-organisms, and recent findings suggest that the cost of fidelity might play a role in the evolution of increased mutation rates. Here, by analysing previously published data from HIV-1 reverse transcriptase in vitro assays, we show a trade-off between enzymatic accuracy and the maximum rate of polymerization, thus providing a biochemical basis

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Ruan, Yongsen, Haiyu Wang, Bingjie Chen, Haijun Wen, and Chung-I. Wu. "Mutations Beget More Mutations—Rapid Evolution of Mutation Rate in Response to the Risk of Runaway Accumulation." Molecular Biology and Evolution 37, no. 4 (2019): 1007–19. http://dx.doi.org/10.1093/molbev/msz283.

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Abstract The rapidity with which the mutation rate evolves could greatly impact evolutionary patterns. Nevertheless, most studies simply assume a constant rate in the time scale of interest (Kimura 1983; Drake 1991; Kumar 2005; Li 2007; Lynch 2010). In contrast, recent studies of somatic mutations suggest that the mutation rate may vary by several orders of magnitude within a lifetime (Kandoth et al. 2013; Lawrence et al. 2013). To resolve the discrepancy, we now propose a runaway model, applicable to both the germline and soma, whereby mutator mutations form a positive-feedback loop. In this

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Scally, Aylwyn. "Mutation rates and the evolution of germline structure." Philosophical Transactions of the Royal Society B: Biological Sciences 371, no. 1699 (2016): 20150137. http://dx.doi.org/10.1098/rstb.2015.0137.

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Genome sequencing studies of de novo mutations in humans have revealed surprising incongruities in our understanding of human germline mutation. In particular, the mutation rate observed in modern humans is substantially lower than that estimated from calibration against the fossil record, and the paternal age effect in mutations transmitted to offspring is much weaker than expected from our long-standing model of spermatogenesis. I consider possible explanations for these discrepancies, including evolutionary changes in life-history parameters such as generation time and the age of puberty, a

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Katz, Sophia, Sarit Avrani, Meitar Yavneh, Sabrin Hilau, Jonathan Gross, and Ruth Hershberg. "Dynamics of Adaptation During Three Years of Evolution Under Long-Term Stationary Phase." Molecular Biology and Evolution 38, no. 7 (2021): 2778–90. http://dx.doi.org/10.1093/molbev/msab067.

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Abstract Many bacterial species that cannot sporulate, such as the model bacterium Escherichia coli, can nevertheless survive for years, following exhaustion of external resources, in a state termed long-term stationary phase (LTSP). Here we describe the dynamics of E. coli adaptation during the first three years spent under LTSP. We show that during this time, E. coli continuously adapts genetically through the accumulation of mutations. For nonmutator clones, the majority of mutations accumulated appear to be adaptive under LTSP, reflected in an extremely convergent pattern of mutation accum

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Amicone, Massimo, Vítor Borges, Maria João Alves, et al. "Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution." Evolution, Medicine, and Public Health 10, no. 1 (2022): 142–55. http://dx.doi.org/10.1093/emph/eoac010.

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Abstract Background and objectives To understand how organisms evolve, it is fundamental to study how mutations emerge and establish. Here, we estimated the rate of mutation accumulation of SARS-CoV-2 in vitro and investigated the repeatability of its evolution when facing a new cell type but no immune or drug pressures. Methodology We performed experimental evolution with two strains of SARS-CoV-2, one carrying the originally described spike protein (CoV-2-D) and another carrying the D614G mutation that has spread worldwide (CoV-2-G). After 15 passages in Vero cells and whole genome sequencin

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Maddamsetti, Rohan, and Nkrumah A. Grant. "Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli." Genome Biology and Evolution 12, no. 9 (2020): 1591–603. http://dx.doi.org/10.1093/gbe/evaa178.

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Abstract All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM. 2017. The dynamics of molecular evolution over 60,000 generations. Nature 551(7678):45–50.), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic dif

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Orr, Adam J., Amanda Padovan, David Kainer, et al. "A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant." Proceedings of the Royal Society B: Biological Sciences 287, no. 1922 (2020): 20192364. http://dx.doi.org/10.1098/rspb.2019.2364.

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Somatic mutations can have important effects on the life history, ecology, and evolution of plants, but the rate at which they accumulate is poorly understood and difficult to measure directly. Here, we develop a method to measure somatic mutations in individual plants and use it to estimate the somatic mutation rate in a large, long-lived, phenotypically mosaic Eucalyptus melliodora tree. Despite being 100 times larger than Arabidopsis, this tree has a per-generation mutation rate only ten times greater, which suggests that this species may have evolved mechanisms to reduce the mutation rate

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Galtier, Nicolas, Richard W. Jobson, Benoît Nabholz, Sylvain Glémin, and Pierre U. Blier. "Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolution." Biology Letters 5, no. 3 (2009): 413–16. http://dx.doi.org/10.1098/rsbl.2008.0662.

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The evolutionary rate of mitochondrial DNA (mtDNA) is highly variable across lineages in animals, and particularly in mammals. This variation has been interpreted as reflecting variations in metabolic rate: mitochondrial respiratory activity would tend to generate mutagenic agents, thus increasing the mutation rate. Here we review recent evidence suggesting that a direct, mechanical effect of species metabolic rate on mtDNA evolutionary rate is unlikely. We suggest that natural selection could act to reduce the (somatic) mtDNA mutation rate in long-lived species, in agreement with the mitochon

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O'Brien, Siobhán, Antonio M. M. Rodrigues, and Angus Buckling. "The evolution of bacterial mutation rates under simultaneous selection by interspecific and social parasitism." Proceedings of the Royal Society B: Biological Sciences 280, no. 1773 (2013): 20131913. http://dx.doi.org/10.1098/rspb.2013.1913.

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Many bacterial populations harbour substantial numbers of hypermutable bacteria, in spite of hypermutation being associated with deleterious mutations. One reason for the persistence of hypermutators is the provision of novel mutations, enabling rapid adaptation to continually changing environments, for example coevolving virulent parasites. However, hypermutation also increases the rate at which intraspecific parasites (social cheats) are generated. Interspecific and intraspecific parasitism are therefore likely to impose conflicting selection pressure on mutation rate. Here, we combine theor

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Boezen, Dieke, Ghulam Ali, Manli Wang, et al. "Empirical estimates of the mutation rate for an alphabaculovirus." PLOS Genetics 18, no. 6 (2022): e1009806. http://dx.doi.org/10.1371/journal.pgen.1009806.

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Mutation rates are of key importance for understanding evolutionary processes and predicting their outcomes. Empirical mutation rate estimates are available for a number of RNA viruses, but few are available for DNA viruses, which tend to have larger genomes. Whilst some viruses have very high mutation rates, lower mutation rates are expected for viruses with large genomes to ensure genome integrity. Alphabaculoviruses are insect viruses with large genomes and often have high levels of polymorphism, suggesting high mutation rates despite evidence of proofreading activity by the replication mac

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Boezen, Dieke, Ghulam Ali, Manli Wang, et al. "Empirical estimates of the mutation rate for an alphabaculovirus." PLOS Genetics 18, no. 6 (2022): e1009806. http://dx.doi.org/10.1371/journal.pgen.1009806.

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Mutation rates are of key importance for understanding evolutionary processes and predicting their outcomes. Empirical mutation rate estimates are available for a number of RNA viruses, but few are available for DNA viruses, which tend to have larger genomes. Whilst some viruses have very high mutation rates, lower mutation rates are expected for viruses with large genomes to ensure genome integrity. Alphabaculoviruses are insect viruses with large genomes and often have high levels of polymorphism, suggesting high mutation rates despite evidence of proofreading activity by the replication mac

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Gong, Yi, R. C. Woodruff, and J. N. Thompson. "Deleterious genomic mutation rate for viability in Drosophila melanogaster using concomitant sibling controls." Biology Letters 1, no. 4 (2005): 492–95. http://dx.doi.org/10.1098/rsbl.2005.0364.

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New deleterious mutations may reduce health and fitness and are involved in the evolution and maintenance of numerous biological processes. Hence, it is important to estimate the deleterious genomic mutation rate ( U ) in representative higher organisms. However, these estimated rates vary widely, mainly because of inadequate experimental controls. Here we describe an experimental design (the Binscy assay) with concomitant sibling controls and estimate U for viability in Drosophila melanogaster to be 0.31. This estimate, like most published studies, focuses on viability mutations and the overa

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Thornlow, Bryan P., Josh Hough, Jacquelyn M. Roger, Henry Gong, Todd M. Lowe, and Russell B. Corbett-Detig. "Transfer RNA genes experience exceptionally elevated mutation rates." Proceedings of the National Academy of Sciences 115, no. 36 (2018): 8996–9001. http://dx.doi.org/10.1073/pnas.1801240115.

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Transfer RNAs (tRNAs) are a central component for the biological synthesis of proteins, and they are among the most highly conserved and frequently transcribed genes in all living things. Despite their clear significance for fundamental cellular processes, the forces governing tRNA evolution are poorly understood. We present evidence that transcription-associated mutagenesis and strong purifying selection are key determinants of patterns of sequence variation within and surrounding tRNA genes in humans and diverse model organisms. Remarkably, the mutation rate at broadly expressed cytosolic tR

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Nyerges, Ákos, Bálint Csörgő, Gábor Draskovits, et al. "Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance." Proceedings of the National Academy of Sciences 115, no. 25 (2018): E5726—E5735. http://dx.doi.org/10.1073/pnas.1801646115.

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Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. Standard laboratory evolution approaches explore only a small fraction of the sequence space and fail to identify exceedingly rare resistance mutations and combinations thereof. Therefore, new rapid and exhaustive methods are needed to accurately assess the potential of resistance evolution and uncover the underlying mutational mechanisms. Here, we introduce directed evolution with random genomic mutations (DIvERGE)

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Sniegowski, Paul D., and Philip J. Gerrish. "Beneficial mutations and the dynamics of adaptation in asexual populations." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1544 (2010): 1255–63. http://dx.doi.org/10.1098/rstb.2009.0290.

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We discuss the dynamics of adaptive evolution in asexual (clonal) populations. The classical ‘periodic selection’ model of clonal evolution assumed that beneficial mutations are very rare and therefore substitute unfettered into populations as occasional, isolated events. Newer models allow for the possibility that beneficial mutations are sufficiently common to coexist and compete for fixation within populations. Experimental evolution studies in microbes provide empirical support for stochastic models in which both selection and mutation are strong effects and clones compete for fixation; ho

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Koch, Evan M., Rena M. Schweizer, Teia M. Schweizer, et al. "De Novo Mutation Rate Estimation in Wolves of Known Pedigree." Molecular Biology and Evolution 36, no. 11 (2019): 2536–47. http://dx.doi.org/10.1093/molbev/msz159.

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Abstract Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in a pedigree of seven wolves. Putative de novo mutations were discovered by whole-genome sequencing and were verified by Sanger sequencing of parents and offspring. Using stringent filters and an estimate of the false negative rate in the remaining observable genome, we obt

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ALÓS-FERRER, CARLOS, and ILJA NEUSTADT. "BEST-RESPONSE DYNAMICS IN A BIRTH-DEATH MODEL OF EVOLUTION IN GAMES." International Game Theory Review 12, no. 02 (2010): 197–204. http://dx.doi.org/10.1142/s021919891000260x.

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We consider a model of evolution with mutations as in Kandori et al. (1993) [Kandori, M., Mailath, G.J., Rob, R., 1993. Learning, mutation, and long run equilibria in games. Econometrica 61, 29–56], where agents follow best-response decision rules as in Sandholm (1998) [Sandholm, W., 1998. Simple and clever decision rules for a model of evolution. Economics Letters 61, 165–170]. Contrary to those papers, our model gives rise to a birth-death process, which allows explicit computation of the long-run probabilities of equilibria for given values of the mutation rate and the population size. We u

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Jasieniuk, M., and B. D. Maxwell. "Populations genetics and the evolution of herbicide resistance in weeds." Comptes rendus 75, no. 4 (2005): 25–35. http://dx.doi.org/10.7202/706069ar.

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Numerous factors, including mutation, selection, inheritance, mating System, and gene flow are important in the evolution of herbicide resistance in weeds. Spontaneous gene mutation is believed to be the main source of genetic variation for resistance evolution in a geographic region in which resistance has not been detected previously. Despite mutation frequencies that are probably very low, the probability of occurrence of at least a single resistant mutant in a susceptible population may be high for weed species with high fecundities and large population sizes. Subsequent repeated treatment

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Harris, Kelley. "Evidence for recent, population-specific evolution of the human mutation rate." Proceedings of the National Academy of Sciences 112, no. 11 (2015): 3439–44. http://dx.doi.org/10.1073/pnas.1418652112.

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As humans dispersed out of Africa they adapted to new environmental challenges, including changes in exposure to mutagenic solar radiation. Humans in temperate latitudes have acquired light skin that is relatively transparent to UV light, and some evidence suggests that their DNA damage response pathways have also experienced local adaptation. This raises the possibility that different populations have experienced different selective pressures affecting genome integrity. Here, I present evidence that the rate of a particular mutation type has recently increased in the European population, risi

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Lynch, Michael. "The rate of polygenic mutation." Genetical Research 51, no. 2 (1988): 137–48. http://dx.doi.org/10.1017/s0016672300024150.

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SummaryBy application of the neutral model of phenotypic evolution, quantitative estimates of the rate of input of genetic variance by polygenic mutation can be extracted from divergence experiments as well as from the response of an inbred base population to selection. The analytical methods are illustrated through a survey of data on a diversity of organisms including Drosophila, Tribolium, mice, and several crop species. The mutational rate of introduction of genetic variance (Vm) scaled by the environmental variance (VE) is shown to vary between populations, species, and characters with a

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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 (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

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Bachar, Amit, Elad Itzhaki, Shmuel Gleizer, Melina Shamshoom, Ron Milo, and Niv Antonovsky. "Point mutations in topoisomerase I alter the mutation spectrum in E. coli and impact the emergence of drug resistance genotypes." Nucleic Acids Research 48, no. 2 (2019): 761–69. http://dx.doi.org/10.1093/nar/gkz1100.

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Abstract Identifying the molecular mechanisms that give rise to genetic variation is essential for the understanding of evolutionary processes. Previously, we have used adaptive laboratory evolution to enable biomass synthesis from CO2 in Escherichia coli. Genetic analysis of adapted clones from two independently evolving populations revealed distinct enrichment for insertion and deletion mutational events. Here, we follow these observations to show that mutations in the gene encoding for DNA topoisomerase I (topA) give rise to mutator phenotypes with characteristic mutational spectra. Using g

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Tanaka, Mark M., Carl T. Bergstrom, and Bruce R. Levin. "The Evolution of Mutator Genes in Bacterial Populations: The Roles of Environmental Change and Timing." Genetics 164, no. 3 (2003): 843–54. http://dx.doi.org/10.1093/genetics/164.3.843.

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Abstract Recent studies have found high frequencies of bacteria with increased genomic rates of mutation in both clinical and laboratory populations. These observations may seem surprising in light of earlier experimental and theoretical studies. Mutator genes (genes that elevate the genomic mutation rate) are likely to induce deleterious mutations and thus suffer an indirect selective disadvantage; at the same time, bacteria carrying them can increase in frequency only by generating beneficial mutations at other loci. When clones carrying mutator genes are rare, however, these beneficial muta

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Ho, Eddie K. H., Fenner Macrae, Leigh C. Latta, et al. "High and Highly Variable Spontaneous Mutation Rates in Daphnia." Molecular Biology and Evolution 37, no. 11 (2020): 3258–66. http://dx.doi.org/10.1093/molbev/msaa142.

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Abstract The rate and spectrum of spontaneous mutations are critical parameters in basic and applied biology because they dictate the pace and character of genetic variation introduced into populations, which is a prerequisite for evolution. We use a mutation–accumulation approach to estimate mutation parameters from whole-genome sequence data from multiple genotypes from multiple populations of Daphnia magna, an ecological and evolutionary model system. We report extremely high base substitution mutation rates (µ-n,bs = 8.96 × 10−9/bp/generation [95% CI: 6.66–11.97 × 10−9/bp/generation] in th

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Garvin, Michael R., and Anthony J. Gharrett. "Evolution: are the monkeys’ typewriters rigged?" Royal Society Open Science 1, no. 2 (2014): 140172. http://dx.doi.org/10.1098/rsos.140172.

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Evolution is presumed to proceed by random mutations, which increase an individual’s fitness. Increased fitness produces a higher survival rate for those individuals within populations and drives the variants to fixation over large timescales to produce new species. We recently identified positively selected sites in mitochondrial complex I in numerous, diverse taxa. In one taxon, a simple sequence repeat (SSR) encompassed the positively selected sites. We hypothesized a model in which: (i) slip-strand mis-pairing during replication due to the SSR increases the mutation rate at these sites, an

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Nicholson, Michael D., David Cheek, and Tibor Antal. "Sequential mutations in exponentially growing populations." PLOS Computational Biology 19, no. 7 (2023): e1011289. http://dx.doi.org/10.1371/journal.pcbi.1011289.

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Stochastic models of sequential mutation acquisition are widely used to quantify cancer and bacterial evolution. Across manifold scenarios, recurrent research questions are: how many cells are there with n alterations, and how long will it take for these cells to appear. For exponentially growing populations, these questions have been tackled only in special cases so far. Here, within a multitype branching process framework, we consider a general mutational path where mutations may be advantageous, neutral or deleterious. In the biologically relevant limiting regimes of large times and small m

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Otto, S. P., and M. E. Orive. "Evolutionary consequences of mutation and selection within an individual." Genetics 141, no. 3 (1995): 1173–87. http://dx.doi.org/10.1093/genetics/141.3.1173.

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Abstract Whether in sexual or asexual organisms, selection among cell lineages during development is an effective way of eliminating deleterious mutations. Using a mathematical analysis, we find that relatively small differences in cell replication rates during development can translate into large differences in the proportion of mutant cells within the adult, especially when development involves a large number of cell divisions. Consequently, intraorganismal selection can substantially reduce the deleterious mutation rate observed among offspring as well as the mutation load within a populati

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