Constant Mutation Rate Research Articles

Somatic mutation rates scale with time not growth rate in long-lived tropical trees

The rates of appearance of new mutations play a central role in evolution. However, mutational processes in natural environments and their relationship with growth rates are largely unknown, particular in tropical ecosystems with high biodiversity. Here, we examined the somatic mutation landscapes of two tropical trees, Shorea laevis (slow-growing) and S. leprosula (fast-growing), in central Borneo, Indonesia. Using newly constructed genomes, we identified a greater number of somatic mutations in tropical trees than in temperate trees. In both species, we observed a linear increase in the number of somatic mutations with physical distance between branches. However, we found that the rate of somatic mutation accumulation per meter of growth was 3.7-fold higher in S. laevis than in S. leprosula. This difference in the somatic mutation rate was scaled with the slower growth rate of S. laevis compared to S. leprosula, resulting in a constant somatic mutation rate per year between the two species. We also found that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. These findings suggest that somatic mutations accumulate with absolute time and older trees have a greater contribution towards generating genetic variation.

Somatic mutation rates scale with time not growth rate in long-lived tropical trees.

The rates of appearance of new mutations play a central role in evolution. However, mutational processes in natural environments and their relationship with growth rates are largely unknown, particular in tropical ecosystems with high biodiversity. Here, we examined the somatic mutation landscapes of two tropical trees, Shorea laevis (slow-growing) and S. leprosula (fast-growing), in central Borneo, Indonesia. Using newly constructed genomes, we identified a greater number of somatic mutations in tropical trees than in temperate trees. In both species, we observed a linear increase in the number of somatic mutations with physical distance between branches. However, we found that the rate of somatic mutation accumulation per meter of growth was 3.7-fold higher in S. laevis than in S. leprosula. This difference in the somatic mutation rate was scaled with the slower growth rate of S. laevis compared to S. leprosula, resulting in a constant somatic mutation rate per year between the two species. We also found that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. These findings suggest that somatic mutations accumulate with absolute time and older trees have a greater contribution towards generating genetic variation.

Estimating mutation rates in a Markov branching process using approximate Bayesian computation

Estimating microbial mutation rates is an essential task in evolutionary biology, with wide range applications in related fields such as virology, epidemiology, clinic and public health, and antibiotic research. Significant progress has been made on this research since 1943 when Luria–Delbrück fluctuation analysis was first introduced. However, existing estimators of mutation rates are heavily reliant on model assumptions in fluctuation analysis, and become less applicable to real microbial experiments which deviate from the model assumptions. To overcome this difficulty, we propose to model fluctuation experimental data by a two-type Markov branching process (MBP) and use approximate Bayesian computation (ABC) to estimate the mutation probability parameters. Such an ABC-based mutation rate estimator is based on intensive simulations from the mutation process, thereby taking advantage of modern computing power. Most importantly, its likelihood-free feature allows more complex and realistic setups of the mutation process, especially when the distribution of the number of mutants cannot be easily derived. To further improve computation efficiency, we use a Gaussian process surrogate to substitute the simulator in the ABC algorithm, and call the resulting estimator GPS-ABC. Simulation studies show that, when used to estimate constant mutation rate in MBP, ABC-based estimators generally outperform traditional moment or likelihood-based estimators. When mutations occur in two stages, i.e., in MBP with a piece-wise constant mutation rate function, traditional mutation rate estimators become not applicable, yet GPS-ABC still achieves reasonable estimates. Finally, the proposed GPS-ABC estimator is used to analyze real fluctuation experimental datasets for studying drug resistance.

Mutation Rate and Spectrum of the Silkworm in Normal and Temperature Stress Conditions.

Mutation rate is a crucial parameter in evolutionary genetics. However, the mutation rate of most species as well as the extent to which the environment can alter the genome of multicellular organisms remain poorly understood. Here, we used parents-progeny sequencing to investigate the mutation rate and spectrum of the domestic silkworm (Bombyx mori) among normal and two temperature stress conditions (32 °C and 0 °C). The rate of single-nucleotide mutations in the normal temperature rearing condition was 0.41 × 10-8 (95% confidence interval, 0.33 × 10-8-0.49 × 10-8) per site per generation, which was up to 1.5-fold higher than in four previously studied insects. Moreover, the mutation rates of the silkworm under the stresses are significantly higher than in normal conditions. Furthermore, the mutation rate varies less in gene regions under normal and temperature stresses. Together, these findings expand the known diversity of the mutation rate among eukaryotes but also have implications for evolutionary analysis that assumes a constant mutation rate among species and environments.

Timing the Initiation of Multiple Myeloma

INTRODUCTION: Cancer pathogenesis is usually characterized by a long evolutionary process where genomic driver events accumulate over time, conferring advantage to distinct subclones, allowing their expansion and progression. METHODS: To investigate the multiple myeloma (MM) evolutionary history, we characterized the mutational processes' landscape and activity over time utilizing a large cohort of 89 whole genomes and 973 exomes. To improve the accuracy of mutational signatures analysis, we analyzed both the 3' and 5' nucleotide context of each mutation and we developed the novel fitting algorithm mmSig, which fits the entire mutational catalogue of each patient with the mutational signatures involved in MM pathogenesis. The contribution of each mutational signature was then corrected based on the cosine similarity between the original 96-mutational profile and the reconstructed profile generated without that signature. To reconstruct the genetic evolutionary history of each patient's cancer, we integrated two approaches. First dividing all mutations into clonal (early) or subclonal (late), then subdivided the clonal mutations into duplicated mutations (present on two alleles and therefore acquired before the duplication) or non-duplicated mutations (detected on a single allele), reflecting either pre-gain and post-gain mutations on the minor allele, or post-gain mutations acquired on one of the duplicated alleles. RESULTS Eight mutational signatures were identified, seven of which showed significant similarity with the most recent mutational signature catalogue (i.e SBS1, SBS2, SBS5, SBS8, SBS9, SBS13 and SBS18). The new mutational signature (named SBS-MM1) was observed only among relapsed patients exposed to alkylating agents (i.e melphalan). The etiology of this specific signature was further confirmed by analyzing recent whole genomes public data from human-induced pluripotent stem cells exposed to melphalan (Kucab et al, Cell 2019). Reconstructing the chronological activity of each mutational signature, we identified four different routes to acquire the full mutational spectrum in MM based on the differential temporal activity of AID (SBS9) and APOBEC (SBS2 and SBS13). Our data indicate that AID activity is not limited to the first contact with the GC, but persists in the majority of patients, behaving similarly to a B-memory cells, capable of re-entering the germinal center upon antigen stimulation to undergo clonal expansion several times before MM diagnosis. Next, we confirmed the clock-like nature (i.e constant mutation rate) of SBS5 in MM and other post-germinal center disorders such as chronic lymphocytic leukemia and B-cell lymphomas. Based on the SBS5 mutation rates and the corrected ratio between duplicated and non-duplicated mutations within large chromosomal gains, we could time the acquisition of the first copy number gain during the life history of each MM patient. Intriguingly, the first MM chromosomal duplication was acquired on average 38 years (ranges 11-64) before sample collection. In 23/27 (85%) cases the first multi gain event occurred before 30 years of age, and in 13/27 (48%) before 20 years reflecting a long and slow process potentially influenced and accelerated by extrinsic and intrinsic factors. DISCUSSION Our analysis provides a glimpse into the early stages of myelomagenesis, where acquisition of the first key drivers precedes cancer diagnosis by decades. Defining the time window when transformation occurs opens up for new avenues of research: to identify causal mechanisms of disease initiation and evolution, to better define the optimal time to start therapy, and ultimately develop early prevention strategies. Disclosures Bolli: CELGENE: Honoraria; JANSSEN: Honoraria; GILEAD: Other: Travel expenses. Corradini:Janssen: Honoraria, Other: Travel Costs; Jazz Pharmaceutics: Honoraria; KiowaKirin: Honoraria; Servier: Honoraria; Takeda: Honoraria, Other: Travel Costs; Kite: Honoraria; Novartis: Honoraria, Other: Travel Costs; Gilead: Honoraria, Other: Travel Costs; Roche: Honoraria; Sanofi: Honoraria; BMS: Other: Travel Costs. Anderson:Janssen: Consultancy, Speakers Bureau; Takeda: Consultancy, Speakers Bureau; Celgene: Consultancy, Speakers Bureau; Bristol-Myers Squibb: Other: Scientific Founder; Oncopep: Other: Scientific Founder; Amgen: Consultancy, Speakers Bureau; Sanofi-Aventis: Other: Advisory Board. Moreau:Celgene: Consultancy, Honoraria; Janssen: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; AbbVie: Consultancy, Honoraria. Papaemmanuil:Celgene: Research Funding. Avet-Loiseau:takeda: Consultancy, Other: travel fees, lecture fees, Research Funding; celgene: Consultancy, Other: travel fees, lecture fees, Research Funding. Munshi:Adaptive: Consultancy; Amgen: Consultancy; Celgene: Consultancy; Janssen: Consultancy; Takeda: Consultancy; Oncopep: Consultancy; Abbvie: Consultancy. Landgren:Karyopharm: Membership on an entity's Board of Directors or advisory committees; Theradex: Other: IDMC; Adaptive: Honoraria, Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Merck: Other: IDMC; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding.

Dissimilarity of individual microsatellite profiles under different mutation models: Empirical approach.

Microsatellites (simple sequence repeats, SSRs) still remain popular molecular markers for studying neutral genetic variation. Two alternative models outline how new microsatellite alleles evolve. Infinite alleles model (IAM) assumes that all possible alleles are equally likely to result from a mutation, while stepwise mutation model (SMM) describes microsatellite evolution as stepwise adding or subtracting single repeat units. Genetic relationships between individuals can be analyzed in higher precision when assuming the SMM scenario with allele size differences as a proxy of genetic distance. If population structure is not predetermined in advance, an empirical data analysis usually includes (a) estimating proximity between individual SSR profiles with a selected dissimilarity measure and (b) determining putative genetic structure of a given set of individuals using methods of clustering and/or ordination for the obtained dissimilarity matrix. We developed new dissimilarity indices between SSR profiles of haploid, diploid, or polyploid organisms assuming different mutation models and compared the performance of these indices for determining genetic structure with population data and with simulations. More specifically, we compared SMM with a constant or variable mutation rate at different SSR loci to IAM using data from natural populations of a freshwater bryozoan Cristatella mucedo (diploid), wheat leaf rust Puccinia triticina (dikaryon), and wheat powdery mildew Blumeria graminis (monokaryon). We show that inferences about population genetic structure are sensitive to the assumed mutation model. With simulations, we found that Bruvo's distance performs generally poorly, while the new metrics are capturing the differences in the genetic structure of the populations.

Abstract 5344: Phylogenetic and signature analyses predict treatment response in high-grade serous ovarian cancer

Abstract Background. High-grade serous ovarian cancer (HGSOC) is a heterogeneous cancer where majority of the patients will eventually relapse. Phylogenetic analysis of longitudinal samples can reveal mechanisms leading to chemoresistance in different subclones. Companied with signature analysis timing of major mutations can be estimated. These methods can reveal the origin of the resistance mechanisms and bring knowledge about the heterogeneity in the surviving subclones. Methods. We employed whole genome sequencing in 48 tumor tissue samples from 9 patients with stage IIB -IVB HGSOC treated at the Turku University Hospital, Finland. DNA from 3-7 tumor tissues at diagnosis (debulking surgery or laparoscopy) and interval debulking surgery (NACT treated patients) and/or relapse from each patient was sequenced with coverage of 30-100x. The mutations were detected with MuTect2 and HaplotypeCaller and copy number alterations with Ascat, excluding germline variation using a blood control. The subclonal structures were identified with PyClone and ClonEvol using maximum of 3000 mutations in each patient. Phylogenetic trees explaining largest proportion of the variations were used. Signatures were fitted with the 30 consensus signatures from COSMIC for each tumor sample as well as for major subclones. Results. Each patient was characterized with 7-15 variant clusters (subclones). Largest divergence was detected in ovaries (11-49% of the mutations were ovary spesific) and lymph nodes compared to other tissues. Even left and right ovary can be very different from each other and ovaries exhibit earlier spreading than other sampled sites. Other tissues were spread from clones detected in the ovaries. Constant mutation rate or higher mutation rate during the treatment could not be explained by the detected number of variants between time points. Early clonal BRCA (COSMIC signature 3) with high contribution predicted better response to chemotherapy. Signature 3 has been associated with homologous recombination deficiency and sensitivity to platinum-based chemotherapy. High APOBEC (signature 2 and 13) associates with higher level of diversification of related branches. Patient level heterogeneity does not seem to predict outcome contrary to within sample heterogeneity which was higher in the patients with shorter survival times. Relapses contained late or early branching clones. In one poor outcome case a clone which was enriched in relapses dominated in the patient derived cell line indicating superior viability and cause of chemoresistance. Conclusions. Cancer evolution trees improved mutation signature analyses and relieved clinically relevant differences between HGSOC patients. Early BRCA signature as well as similar signatures between subclones predicted good clinical outcomes. Citation Format: Jaana Oikkonen, Yilin Li, Amjad Alkodsi, Olli Carpen, Kaisa Huhtinen, Sakari Hietanen, Seija E. Grenman, Rainer Lehtonen, Sampsa Hautaniemi. Phylogenetic and signature analyses predict treatment response in high-grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5344.

Application of Evolutionary Computation for Berth Scheduling at Marine Container Terminals: Parameter Tuning Versus Parameter Control

Considering a substantial increase in the international seaborne containerized trade volumes, marine container terminal operators have to improve efficiency of the processes inside their terminals in order to meet the growing demand. An efficient berth scheduling is of a high importance for the terminal’s performance, as it significantly influences the turnaround time of vessels. This paper proposes a novel Evolutionary Algorithm to assist with berth scheduling at marine container terminals that, unlike published to date studies on berth scheduling, applies a parameter control strategy. Specifically, an adaptive mechanism is developed for the mutation operator, in which the mutation rate is altered based on feedback from the search. The objective of the proposed mixed integer model aims to minimize the total weighted vessel service cost. A set of numerical experiments are conducted to assess performance of the developed algorithm based on a comparison against a typical Evolutionary Algorithm that applies a constant mutation rate value, determined from the parameter tuning analysis. Results indicate that the optimality gap does not exceed 0.80% for both algorithms. Furthermore, deployment of the adaptive mechanism for the mutation operator yields an average of 5.4% and 8.5% savings in terms of the total weighted vessel service cost for medium and large size problem instances, respectively, without a significant increase in the computational time.

Spontaneous mutations of a model heterotrophic marine bacterium.

Heterotrophic marine bacterioplankton populations display substantive genomic diversity that is commonly explained to be the result of selective forces imposed by resource limitation or interactions with phage and predators. Here we use a mutation-accumulation experiment followed by whole-genome sequencing of mutation lines to determine an unbiased rate and molecular spectrum of spontaneous mutations for a model heterotrophic marine bacterium in the globally important Roseobacter clade, Ruegeria pomeroyi DSS-3. We find evidence for mutational bias towards deletions over insertions, and this process alone could account for a sizable portion of genome size diversity among roseobacters and also implies that lateral gene transfer and/or selection must also play a role in maintaining roseobacters with large genome sizes. We also find evidence for a mutational bias in favor of changes from A/T to G/C nucleobases, which explains widespread occurrences of G/C-enriched Roseobacter genomes. Using the calculated mutation rate of 1.39 × 10-10 per base per generation, we implement a 'mutation-rate clock' approach to date the evolution of roseobacters by assuming a constant mutation rate along their evolutionary history. This approach gives an estimated date of Roseobacter genome expansion in good agreement with an earlier fossil-based estimate of ~250 million years ago and is consistent with a hypothesis of a correlated evolutionary history between roseobacters and marine eukaryotic phytoplankton groups.

Genomic confirmation of nutrient-dependent mutability of mutators in Escherichia coli.

Mutators with increased mutation rates are prevalent in various environments and have important roles in accelerating adaptive evolution. Previous studies on mutator strains of microorganisms have shown that some mutators have constant mutation rates, whereas others exhibit switchable mutation rates depending on nutritional conditions. This suggests that the contributions of mutators on evolution vary with fluctuating nutritional conditions. However, such conditional mutability has been unclear at the genomic level. In addition, it is still unknown why mutation rates change with nutritional condition. Here, we used two mutator strains of Escherichia coli to explore the nutrient dependence of mutation rates at the genomic level. These strains were transferred repeatedly under different nutritional conditions for hundreds of generations to accumulate mutations. Whole-genome sequencing of the offspring showed that the nutrient dependence of the mutation rates was pervasive at the genomic scale. Neutrality in the mutation accumulation processes and constancy in the mutational bias suggested that nutrient dependence was not derived from conditional selective purges or from shifts of mutational bias. Some mutators could simply switch their mutation rates for both transitions and transversions in response to nutritional shifts.

Insights into transcriptomes of big and low sagebrush.

We report the sequencing and assembly of three transcriptomes from Big (Artemisia tridentata ssp. wyomingensis and A. tridentata ssp. tridentata) and Low (A. arbuscula ssp. arbuscula) sagebrush. The sequence reads are available in the Sequence Read Archive of NCBI. We demonstrate the utilities of these transcriptomes for gene discovery and phylogenomic analysis. An assembly of 61,883 transcripts followed by transcript identification by the program TRAPID revealed 16 transcripts directly related to terpene synthases, proteins critical to the production of multiple secondary metabolites in sagebrush. A putative terpene synthase was identified in two of our sagebrush samples. Using paralogs with synonymous mutations we reconstructed an evolutionary time line of ancient genome duplications. By applying a constant mutation rate to the data we estimate that these three ancient duplications occurred about 18, 34 and 60 million years ago. These transcriptomes offer a foundation for future studies of sagebrush, including inferences in chemical defense and the identification of species and subspecies of sagebrush for restoration and preservation of the threatened sage-grouse.

Elevated germline mutation rate in teenage fathers.

Men age and die, while cells in their germline are programmed to be immortal. To elucidate how germ cells maintain viable DNA despite increasing parental age, we analysed DNA from 24 097 parents and their children, from Europe, the Middle East and Africa. We chose repetitive microsatellite DNA that mutates (unlike point mutations) only as a result of cellular replication, providing us with a natural ‘cell-cycle counter’. We observe, as expected, that the overall mutation rate for fathers is seven times higher than for mothers. Also as expected, mothers have a low and lifelong constant DNA mutation rate. Surprisingly, however, we discover that (i) teenage fathers already set out from a much higher mutation rate than teenage mothers (potentially equivalent to 77–196 male germline cell divisions by puberty); and (ii) ageing men maintain sperm DNA quality similar to that of teenagers, presumably by using fresh batches of stem cells known as ‘A-dark spermatogonia’.

Mitochondrial and Y chromosome haplotype motifs as diagnostic markers of Jewish ancestry: a reconsideration.

Several authors have proposed haplotype motifs based on site variants at the mitochondrial genome (mtDNA) and the non-recombining portion of the Y chromosome (NRY) to trace the genealogies of Jewish people. Here, we analyzed their main approaches and test the feasibility of adopting motifs as ancestry markers through construction of a large database of mtDNA and NRY haplotypes from public genetic genealogical repositories. We verified the reliability of Jewish ancestry prediction based on the Cohen and Levite Modal Haplotypes in their “classical” 6 STR marker format or in the “extended” 12 STR format, as well as four founder mtDNA lineages (HVS-I segments) accounting for about 40% of the current population of Ashkenazi Jews. For this purpose we compared haplotype composition in individuals of self-reported Jewish ancestry with the rest of European, African or Middle Eastern samples, to test for non-random association of ethno-geographic groups and haplotypes. Overall, NRY and mtDNA based motifs, previously reported to differentiate between groups, were found to be more represented in Jewish compared to non-Jewish groups. However, this seems to stem from common ancestors of Jewish lineages being rather recent respect to ancestors of non-Jewish lineages with the same “haplotype signatures.” Moreover, the polyphyly of haplotypes which contain the proposed motifs and the misuse of constant mutation rates heavily affected previous attempts to correctly dating the origin of common ancestries. Accordingly, our results stress the limitations of using the above haplotype motifs as reliable Jewish ancestry predictors and show its inadequacy for forensic or genealogical purposes.

Nutrient-dependent growth defects and mutability of mutators in Escherichia coli.

So-called mutators emerge when mismatch repair and proofreading mechanisms are defective. Mutators not only accelerate the accumulation of mutations that are beneficial for adaptation but also cause a large number of deleterious mutations that are disadvantageous for cell growth. However, such growth defects may be compensated by nutrient availability. How the growth burden is associated with high mutability in relation to nutritional variation is an intriguing question. To address this question, we constructed a variety of Escherichia coli mutator strains through combinatorial deletions of mismatch repair and proofreading genes and quantitatively evaluated their growth and mutation rates under different nutritional conditions. Growth defects caused by high mutation rates were commonly observed in all mutators, and these defects were alleviated by nutrient supplementation in most mutators. In addition, the mutation rates of the mutators fluctuated greatly in response to nutritional conditions, in contrast to the nearly constant mutation rate of the wild-type strain under varying nutritional conditions. The results showed conditional growth defects and nutrition-sensitive mutability as general features of mutators. This study indicates the importance of modulating mutability in response to changing nutrient conditions to minimize the risk of extinction due to genetic load.

On exceptional times for generalized Fleming–Viot processes with mutations

If \(\mathbf Y\) is a standard Fleming–Viot process with constant mutation rate (in the infinitely many sites model) then it is well known that for each \(t>0\) the measure \(\mathbf Y_t\) is purely atomic with infinitely many atoms. However, Schmuland proved that there is a critical value for the mutation rate under which almost surely there are exceptional times at which the stationary version of \(\mathbf Y\) is a finite sum of weighted Dirac masses. In the present work we discuss the existence of such exceptional times for the generalized Fleming–Viot processes. In the case of Beta-Fleming–Viot processes with index \(\alpha \in \,]1,2[\) we show that—irrespectively of the mutation rate and \(\alpha \)—the number of atoms is almost surely always infinite. The proof combines a Pitman–Yor type representation with a disintegration formula, Lamperti’s transformation for self-similar processes and covering results for Poisson point processes.

A population model with non-neutral mutations using branching processes with immigration

We consider a stationary continuous model of random size population with non-neutral mutations using a continuous state branching process with non-homogeneous immigration. We assume the type (or mutation) of the immigrants is random given by a constant mutation rate measure. We determine some genealogical properties of this process such as: distribution of the time to the most recent common ancestor (MRCA), bottleneck effect at the time to the MRCA (which might be drastic for some mutation rate measures), favorable type for the MRCA, asymptotics of the number of ancestors.

Dynamic of Mutational Events in Variable Number Tandem Repeats ofEscherichia coliO157:H7

VNTRs regions have been successfully used for bacterial subtyping; however, the hypervariability in VNTR loci is problematic when trying to predict the relationships among isolates. Since few studies have examined the mutation rate of these markers, our aim was to estimate mutation rates of VNTRs specific for verotoxigenic E. coli O157:H7. The knowledge of VNTR mutational rates and the factors affecting them would make MLVA more effective for epidemiological or microbial forensic investigations. For this purpose, we analyzed nine loci performing parallel, serial passage experiments (PSPEs) on 9 O157:H7 strains. The combined 9 PSPE population rates for the 8 mutating loci ranged from 4.4 × 10−05 to 1.8 × 10−03 mutations/generation, and the combined 8-loci mutation rate was of 2.5 × 10−03 mutations/generation. Mutations involved complete repeat units, with only one point mutation detected. A similar proportion between single and multiple repeat changes was detected. Of the 56 repeat mutations, 59% were insertions and 41% were deletions, and 72% of the mutation events corresponded to O157-10 locus. For alleles with up to 13 UR, a constant and low mutation rate was observed; meanwhile longer alleles were associated with higher and variable mutation rates. Our results are useful to interpret data from microevolution and population epidemiology studies and particularly point out that the inclusion or not of O157-10 locus or, alternatively, a differential weighting data according to the mutation rates of loci must be evaluated in relation with the objectives of the proposed study.

Role of DNA Polymerases in Repeat-Mediated Genome Instability

Expansions of simple DNA repeats cause numerous hereditary diseases in humans. We analyzed the role of DNA polymerases in the instability of Friedreich's ataxia (GAA)(n) repeats in a yeast experimental system. The elementary step of expansion corresponded to ~160 bp in the wild-type strain, matching the size of Okazaki fragments in yeast. This step increased when DNA polymerase α was mutated, suggesting a link between the scale of expansions and Okazaki fragment size. Expandable repeats strongly elevated the rate of mutations at substantial distances around them, a phenomenon we call repeat-induced mutagenesis (RIM). Notably, defects in the replicative DNA polymerases δ and ε strongly increased rates for both repeat expansions and RIM. The increases in repeat-mediated instability observed in DNA polymerase δ mutants depended on translesion DNA polymerases. We conclude that repeat expansions and RIM are two sides of the same replicative mechanism.

Trisomy 12 CLLs progress through NOTCH1 mutations

Trisomy 12 CLLs progress through NOTCH1 mutations

Correcting the Apparent Mutation Rate Acceleration at Shorter Time Scales under a Jukes-Cantor Model

At macroevolutionary time scales, and for a constant mutation rate, there is an expected linear relationship between time and the number of inferred neutral mutations (the "molecular clock"). However, at shorter time scales, a number of recent studies have observed an apparent acceleration in the rate of molecular evolution. We study this apparent acceleration under a Jukes-Cantor model applied to a randomly mating population, and show that, under the model, it arises as a consequence of ignoring short-term effects due to existing diversity within the population. The acceleration can be accounted for by adding the correction term h(0)e(-4μt/3) to the usual Jukes-Cantor formula p(t) = 3/4(1 - e (-(-4μt/3), where h(0) is the expected heterozygosity in the population at time t = 0. The true mutation rate μ may then be recovered, even if h(0) is not known, by estimating μ and h(0) simultaneously using least squares. Rate estimates made without the correction term (i.e., incorrectly assuming the population to be homogeneous) will result in a divergent rate curve of the form μ(div) = μ + C/t, so that the mutation rate appears to approach infinity as the time scale approaches zero. Although our quantitative results apply only to the Jukes-Cantor model, it is reasonable to suppose that the qualitative picture that emerges also applies to more complex models. Our study, therefore, demonstrates the importance of properly accounting for any ancestral diversity, because it may otherwise play a dominant role in rate overestimation.