The Genetic Basis of Phenotypic Adaptation I: Fixation of Beneficial Mutations in the Moving Optimum Model

We study the genetic basis of adaptation in a moving optimum model, in which the optimal value for a quantitative trait increases over time at a constant rate. We first analyze a one-locus two-allele model with recurrent mutation, for which we derive accurate analytical approximations for (i) the time at which a previously deleterious allele becomes beneficial, (ii) the waiting time for a successful new mutation, and (iii) the time the mutant allele needs to reach fixation. On the basis of these results, we show that the shortest total time to fixation is for alleles with intermediate phenotypic effect. We derive an approximation for this “optimal” effect, and we show that it depends in a simple way on a composite parameter, which integrates the ecological parameters and the genetic architecture of the trait. In a second step, we use stochastic computer simulations of a multilocus model to study the order in which mutant alleles with different effects go to fixation. In agreement with the one-locus results, alleles with intermediate effect tend to become fixed earlier than those with either small or large effects. However, the effect size of the fastest mutations differs from the one predicted in the one-locus model. We show how these differences can be explained by two specific effects of multilocus genetics. Finally, we discuss our results in the light of three relevant timescales acting in the system—the environmental, mutation, and fixation timescales—which define three parameter regimes leading to qualitative differences in the adaptive substitution pattern.     

A Ruby in the Rubbish: Beneficial Mutations, Deleterious Mutations and the Evolution of Sex

This study presents a mathematical model in which a single beneficial mutation arises in a very large population that is subject to frequent deleterious mutations. The results suggest that, if the population is sexual, then the deleterious mutations will have little effect on the ultimate fate of the beneficial mutation. However, if most offspring are produced asexually, then the probability that the beneficial mutation will be lost from the population may be greatly enhanced by the deleterious mutations. Thus, sexual populations may adapt much more quickly than populations where most reproduction is asexual. Some of the results were produced using computer simulation methods, and a technique was developed that allows treatment of arbitrarily large numbers of individuals in a reasonable amount of computer time. This technique may be of prove useful for the analysis of a wide variety of models, though there are some constraints on its applicability. For example, the technique requires that reproduction can be described by Poisson processes.     

The Consistency of Beneficial Fitness Effects of Mutations across Diverse Genetic Backgrounds

Parallel and convergent evolution have been remarkably common observations in molecular adaptation but primarily in the context of the same genotype adapting to the same conditions. These phenomena therefore tell us about the stochasticity and limitations of adaptation. The limited data on convergence and parallelism in the adaptation of different genotypes conflict as to the importance of such events. If the effects of beneficial mutations are highly context dependent (i.e., if they are epistatic), different genotypes should adapt through different mutations. Epistasis for beneficial mutations has been investigated but mainly through measurement of interactions between individually beneficial mutations for the same genotype. We examine epistasis for beneficial mutations at a broader genetic scale by measuring the fitness effects of two mutations beneficial for the ssDNA bacteriophage ID11 in eight different, related genotypes showing 0.3-3.7% nucleotide divergence from ID11. We found no evidence for sign epistasis, but the mutations tended to have much smaller or no effects on fitness in the new genotypes. We found evidence for diminishing-returns epistasis; the effects were more beneficial for lower-fitness genotypes. The patterns of epistasis were not determined by phylogenetic relationships to the original genotype. To improve our understanding of the patterns of epistasis, we fit the data to a model in which each mutation had a constant, nonepistatic phenotypic effect across genotypes and the phenotype-fitness map had a single optimum. This model fit the data well, suggesting that epistasis for these mutations was due to nonlinearity in the phenotype-fitness mapping and that the likelihood of parallel evolution depends more on phenotype than on genotype.     

A Method for Estimating Penetrance of Pathogenic Mutations in a Mitochondrial Genome

Variation in the age of onset is typical of many mitochondrial diseases. The estimation of penetrance of deleterious mtDNA mutations causing such diseases is usually conducted on samples of individuals whose age exceeds the maximum age of the disease manifestation. In the case of rare diseases, samples of sufficient size sometimes cannot be formed. In this study, we propose a method for estimating penetrance involving individuals of any age. The efficiency of the method is demonstrated using Leber hereditary optic neuropathy as an example. It is shown that the method provides an unbiased estimate of penetrance and considerably reduces the error of this estimate in comparison with a sample including individuals whose age exceeds the maximum age of disease manifestation.     

A Stochastic Model for Estimating Adolescent Sterility

In this article, a simple stochastic model for the time to first conception of a cohort of married women is developed, by identifying three states, ‘adolescent sterile’, ‘ovulating’ and ‘conceived‘, into which they can be placed. It is demonstrated that the model provides a close fit to observed data. The estimates of the parameters in the model, can be used to calculate the number of women in each state at different points of time and also to obtain estimates of the probabilities of conception for the two categories of women, adolescent sterile and biologically mature.     

Activating Mutations of the TRPML1 Channel Revealed by Proline-scanning Mutagenesis

The mucolipin TRP (TRPML) proteins are a family of endolysosomal cation channels with genetically established importance in humans and rodent. Mutations of human TRPML1 cause type IV mucolipidosis, a devastating pediatric neurodegenerative disease. Our recent electrophysiological studies revealed that, although a TRPML1-mediated current can only be recorded in late endosome and lysosome (LEL) using the lysosome patch clamp technique, a proline substitution in TRPML1 (TRPML1^V432P) results in a large whole cell current. Thus, it remains unknown whether the large TRPML1^V432P-mediated current results from an increased surface expression (trafficking), elevated channel activity (gating), or both. Here we performed systemic Pro substitutions in a region previously implicated in the gating of various 6 transmembrane cation channels. We found that several Pro substitutions displayed gain-of-function (GOF) constitutive activities at both the plasma membrane (PM) and endolysosomal membranes. Although wild-type TRPML1 and non-GOF Pro substitutions localized exclusively in LEL and were barely detectable in the PM, the GOF mutations with high constitutive activities were not restricted to LEL compartments, and most significantly, exhibited significant surface expression. Because lysosomal exocytosis is Ca²⁺-dependent, constitutive Ca²⁺ permeability due to Pro substitutions may have resulted in stimulus-independent intralysosomal Ca²⁺ release, hence the surface expression and whole cell current of TRPML1. Indeed, surface staining of lysosome-associated membrane protein-1 (Lamp-1) was dramatically increased in cells expressing GOF TRPML1 channels. We conclude that TRPML1 is an inwardly rectifying, proton-impermeable, Ca²⁺ and Fe²⁺/Mn²⁺ dually permeable cation channel that may be gated by unidentified cellular mechanisms through a conformational change in the cytoplasmic face of the transmembrane 5 (TM5). Furthermore, activation of TRPML1 in LEL may lead to the appearance of TRPML1 proteins at the PM.     

A High Frequency of Beneficial Mutations Across Multiple Fitness Components in Saccharomyces cerevisiae

Mutation-accumulation experiments are widely used to estimate parameters of spontaneous mutations affecting fitness. In many experiments only one component of fitness is measured. In a previous study involving the diploid yeast Saccharomyces cerevisiae, we measured the growth rate of 151 mutation-accumulation lines to estimate parameters of mutation. We found that an unexpectedly high frequency of fitness-altering mutations was beneficial. Here, we build upon our previous work by examining sporulation efficiency, spore viability, and haploid growth rate and find that these components of fitness also show a high frequency of beneficial mutations. We also examine whether mutation-acycumulation (MA) lines show any evidence of pleiotropy among accumulated mutations and find that, for most, there is none. However, MA lines that have zero fitness (i.e., lethality) for any one fitness component do show evidence for pleiotropy among accumulated mutations. We also report estimates of other parameters of mutation based on each component of fitness.ADAPTATION can occur from standing genetic variation or from newly arising mutations. The relative importance of these two sources of adaptive mutations is affected by a variety of factors, including those that alter standing levels of genetic variation (see Barrett and Schluter 2008) and those that generate new mutations. Predicting how quickly a population will adapt and the type of beneficial mutations that will fuel that adaptation requires estimates of the additive genetic variance in fitness and of the beneficial mutation rate and the distribution of beneficial effects. While additive genetic variance for fitness has been estimated in a variety of organisms (Mousseau and Roff 1987), the beneficial mutation rate and the distribution of beneficial effects have only been estimated in a few studies (Shaw et al. 2002; Joseph and Hall 2004; Perfeito et al. 2007; Dickinson 2008; Hall et al. 2008). Surprisingly, these studies estimate that between 6 (Joseph and Hall 2004) and 50% (Shaw et al. 2002) of fitness-altering mutations are beneficial. In contrast, most mutation-accumulation (MA) experiments identify few, if any, beneficial mutations. Such wildly different estimates have even been generated from studies of the same species in similar environments (Zeyl and Devisser 2001; Joseph and Hall 2004; Dickinson 2008; Hall et al. 2008). If these estimates are correct, then they would suggest that the genotypes used in these experiments have vastly different evolutionary potential with respect to their capacity to exhibit rapid adaptation from new mutations.A more likely scenario is that much of the variation in estimates of the beneficial mutation rate is due to methodological differences between studies. One possibility is the fitness component being analyzed. The beneficial mutation rate may be under- or overestimated if the fitness component is under stabilizing selection or subject to antagonistic pleiotropy. Analyses of mutation-accumulation data typically assume that selection is directional. As a result, analyses of phenotypes under stabilizing selection may falsely conclude that mutations that increase a phenotype are beneficial and mutations that lower values are deleterious (see Keightley and Lynch''s 2003 criticism of Shaw et al. 2002). Alternatively, the beneficial mutation rate may be over- (or under) estimated if mutations increase fitness in regard to one component, but lower fitness in regard to lifetime fitness or another fitness component (i.e., antagonistic pleiotropy). Here, we explore these possibilities by investigating whether the high beneficial mutation rates estimated from our previous experiments are specific to the fitness component that we examined.In two previous studies we accumulated mutations in 152 yeast, MA lines and used measures of their effects on diploid growth rate to estimate parameters of beneficial and deleterious mutations. In the first study we estimated that 6% of mutations accumulated during the first 1012 generations of accumulation improved diploid growth (Joseph and Hall 2004). To determine whether this high beneficial mutation rate was due to sampling error, we passaged the lines for an additional 1050 generations and found that 13% of mutations improved diploid growth (Hall et al. 2008). Similarly, another yeast MA experiment (Dickinson 2008) estimated an uncorrected frequency of beneficial mutations of 25%, although correction for within-colony selection reduces this estimate by approximately half. Together, these studies indicate that a substantial proportion of mutations accumulated in these yeast MA lines are beneficial for a single fitness component and that this observation cannot be explained by the chance sampling of a few beneficial mutations.In this study we return to our yeast MA lines (Joseph and Hall 2004) and examine whether the high beneficial mutation rate that we estimated after 1012 generations is an artifact of the fitness component that we examined. To test this hypothesis we examined whether our MA lines carry mutations that are beneficial across multiple fitness components: diploid growth, sporulation efficiency, spore viability, and haploid growth rate. If our previous results are due to us analyzing a fitness component that is either subject to stabilizing selection or antagonistic pleiotropy, then mutations accumulated in our lines will be conditionally beneficial and analyses of additional fitness components would yield different estimates of the beneficial mutation rate. We found that three of the four fitness components yield high estimates of the beneficial mutation rate. This suggests that multiple MA lines have accumulated beneficial mutations and that the high beneficial mutation rate that we previously estimated is not an artifact of the fitness component that we examined.Measuring multiple components of fitness also allowed us to examine the pleiotropic effects of beneficial and deleterious mutations. In general, we found that mutations altering one component of fitness have little effect on other components. However, lethal mutations were typically pleiotropic.

Conclusions:

We find that for three of four fitness components examined, a high frequency of spontaneous, fitness-altering mutations in diploid yeast is beneficial. Further, we do not detect pleiotropy of small-effect mutations, while lethal mutations show high levels of pleiotropy. In most cases, pleiotropy is positive. Two lines show evidence of antagonistic pleiotropy, indicating trade-offs, although heterozygote advantage cannot be ruled out.     

遗传参数不同估计方法的比较

利用模拟方法比较了5种方差组分估计方法(ANOVA,Henderson-Ⅲ,MLMT,R EMLMT和MIVQUE)对遗传参数的估计效果。结果表明:REMLMT法在各种情况下均能得到较好的参数估值,估计的准确度相对较高;ANOVA方法在小群体和不均衡资料情况下估计效果最差。同时,群体含量和结构能影响各种方法的估计效果, 群体含量较小或资料来源的公畜数太少,将导致遗传参数的估计误差增大,准确性降低。 Abstract:Five methods for estimating components of (Co) variance,including ANOVA,Henderson-III,MLMT,REMLMT and MIVQUE were compared using computer simulation.The results showed that REMLMT could obtain more accurate estimates for all data sets,while the estimates obtained by ANOVA always had greater deviations from the true values,especial for small and well-unbalanced data sets.Also,the effects of estimation were dependent on structure of population size,accuracy of estimates would be decreased when number of sires was too few or data contained small number of animals.     

Perspective on Mutagenesis and Repair: The Standard Model and Alternate Modes of Mutagenesis

ABSTRACT

The basic ideas of replication, mutagenesis, and repair have outlined a picture of how point mutations occur that has provided a valuable framework for theory and experiment, much as the Standard Model of particle physics has done for our concept of fundamental particles. However, alternative modes of mutagenesis are being defined that are changing our perspective of the “Standard Model” of mutagenesis, requiring an expanded model. The genome is now envisioned as being in dynamic equilibrium between a multitude of forces for mutational change and forces that counteract such change. By maintaining a delicate balance between these forces, cells avoid unwanted or excessive mutations. Yet, cells allow mutagenesis to occur under certain conditions. We can define an emerging paradigm. Namely, mechanisms exist that can direct point mutations to specific designated genes or regions of genes. In some cases, this is achieved by specific enzymes, and in other cases high mutability is programmed into the sequence of certain genes to help generate diversity. In yet additional cases, general mutability is increased under stress, and selective forces allow the recovery of favorable mutants.     

Lack of Evidence for Sign Epistasis Between Beneficial Mutations in an RNA Bacteriophage

In previous work (Betancourt, Genetics 181:1535, 2009), I propagated three large laboratory populations of an RNA phage (MS2) as they adapted to a controlled laboratory environment. These populations were large enough so that evolution might be expected to be mostly repeatable, but they nevertheless fixed different suites of mutations over the course of the experiment. Here, I investigate one possible explanation for these results: epistasis, in which the effect of a mutation depends on its genetic background, may have prevented populations with different initial substitutions from fixing the same set of subsequent mutations. I show that two mutations that previously occurred in different genetic backgrounds are beneficial on either background. This result suggests that sign epistasis-in which a mutation is beneficial on one background, but deleterious on another-is not the cause of different evolutionary trajectories observed in the Betancourt (2009) experiment. However, they can be explained by either magnitude epistasis-in which mutations have stronger or weaker beneficial effects depending on the background-or by the simultaneous fixation of multiple beneficial mutations. Surprisingly, the large populations of the previous experiment showed less parallel evolution than the small populations of this experiment, which lends support to the fixation of multiple beneficial mutations contributing to the patterns seen in both experiments.     

A Search for Genetic Loci Responsible for Stress-Induced Arterial Hypertension in the ISIAH Rats

Hypertension is a widespread human disease caused by a complex interaction of a series of the genetic factors with both each other and the environmental conditions. In this study we aimed at determining the candidate genetic loci responsible for hypertension in the ISIAH rats and studying the dynamics of the relevant genetic and physiological mechanisms in rat ontogeny. The candidate genetic loci were identified from association of the microsatellite markers linked to these loci with arterial hypertension in rat F₂ hybrids exposed to stress. Two populations of F₂ hybrids of different age (3–4 and 6 months) were obtained by crossing hypertensive ISIAH and normotensive WAG rats. We present the results of cosegregation analysis for the following loci: the gene for the Na⁺, K⁺-ATPase alpha 1 subunit (Atp1a1), the endothelin-2 gene (Edn2), the low affinity nerve growth factor receptor gene (Lngfr), and a region of chromosome 10 marked with the D10Rat58 microsatellile located 3 cM away of the aldolase C gene (AldC). The results obtained allowed us to localize the genes responsible for the stress-induced arterial hypertension in the ISIAH rats to the Atp1a1locus (P < 0.05), chromosome 2 and to the Lngfr gene locus (P < 0.05), chromosome 10. The association of hypertensive status with the Lngfr gene was found only in young ISIAH rats whereas in adult rats of this strain, hypertension was associated with the Atp1a1locus.     

Empirical Complexities in the Genetic Foundations of Lethal Mutagenesis

From population genetics theory, elevating the mutation rate of a large population should progressively reduce average fitness. If the fitness decline is large enough, the population will go extinct in a process known as lethal mutagenesis. Lethal mutagenesis has been endorsed in the virology literature as a promising approach to viral treatment, and several in vitro studies have forced viral extinction with high doses of mutagenic drugs. Yet only one empirical study has tested the genetic models underlying lethal mutagenesis, and the theory failed on even a qualitative level. Here we provide a new level of analysis of lethal mutagenesis by developing and evaluating models specifically tailored to empirical systems that may be used to test the theory. We first quantify a bias in the estimation of a critical parameter and consider whether that bias underlies the previously observed lack of concordance between theory and experiment. We then consider a seemingly ideal protocol that avoids this bias—mutagenesis of virions—but find that it is hampered by other problems. Finally, results that reveal difficulties in the mere interpretation of mutations assayed from double-strand genomes are derived. Our analyses expose unanticipated complexities in testing the theory. Nevertheless, the previous failure of the theory to predict experimental outcomes appears to reside in evolutionary mechanisms neglected by the theory (e.g., beneficial mutations) rather than from a mismatch between the empirical setup and model assumptions. This interpretation raises the specter that naive attempts at lethal mutagenesis may augment adaptation rather than retard it.     

Quantitative Trait Loci Identification by Estimating the Genetic Model based on the Extremal Samples

Background In genetic association studies with quantitative trait loci (QTL), the association between a candidate genetic marker and the trait of interest is commonly examined by the omnibus F test or by the t-test corresponding to a given genetic model or mode of inheritance. It is known that the t-test with a correct model specification is more powerful than the F test. However, since the underlying genetic model is rarely known in practice, the use of a model-specific t-test may incur substantial power loss. Robust-efficient tests, such as the Maximin Efficiency Robust Test (MERT) and MAX3 have been proposed in the literature.Methods In this paper, we propose a novel two-step robust-efficient approach, namely, the genetic model selection (GMS) method for quantitative trait analysis. GMS selects a genetic model by testing Hardy-Weinberg disequilibrium (HWD) with extremal samples of the population in the first step and then applies the corresponding genetic model-specific t-test in the second step.Results Simulations show that GMS is not only more efficient than MERT and MAX3, but also has comparable power to the optimal t-test when the genetic model is known.Conclusion Application to the data from Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort demonstrates that the proposed approach can identify meaningful biological SNPs on chromosome 19.     

Genetic Analysis of Mouse T Haplotypes Using Mutations Induced by Ethylnitrosourea Mutagenesis: The Order of T and Qk Is Inverted in T Mutants

The t region of mouse chromosome 17 exhibits recombination suppression with wild-type chromatin. However, the region has resisted classical genetic dissection because of a lack of defined variants. Mutations induced by N-ethyl-N-nitrosourea (ENU) at the Brachyury (T), quaking (qk), and tufted (tf) loci of the mouse tw5 haplotype have now allowed the analysis of crossovers between two complete t haplotypes. A classical breeding analysis of the complete t haplotypes, tw5 and t12, utilizing the newly induced markers, reveals two inversions in t chromatin: one involving T and qk, and one involving tf and the H-2 complex. Moreover, the recombination frequency between the loci of T and qk is reduced compared to the frequency reported in normal chromatin. These two inversions are a sufficient explanation for the recombination inhibition with normal chromatin exhibited by t haplotypes isolated from the wild. Furthermore, the reduced recombination frequency between T and qk may indicate that the proximal gene rearrangement is not a simple inversion.     

转座子Tn917诱变的炭疽杆菌芽孢形成缺陷株的筛选

目的:诱导转座子Tn917随机插入炭疽杆菌染色体,产生在不同位点突变的突变体库,从中筛选芽孢形成缺陷型突变株。方法:用含转座子Tn917的质粒pLTV3转化炭疽杆菌,以低浓度红霉素诱导转座因发生转座,产生大量的突变株。进而用氯化三苯基四氮唑染色法和复红美蓝染色法从突变体库中筛选芽孢形成缺陷株;用Southern杂交法对芽孢形成缺陷株进行验证。结果:对2000个突变体进行了筛选,共得到6株芽孢形成缺陷株,在LB培养基中培养5d后,镜下仍未见有芽孢形成,呈现明显的芽孢形成缺陷特征。Southern杂交表明野生株无杂交带,突变株均有且只有1条杂交带,且杂交带的位置不尽相同。结论:转座子Tn917可以单拷贝随机诱变炭疽杆菌野生株,产生在不同位点突变的突变株。     

A Hierarchical Model for Estimating Change in American Woodcock Populations

Abstract The Singing-Ground Survey (SGS) is a primary source of information on population change for American woodcock (Scolopax minor). We analyzed the SGS using a hierarchical log-linear model and compared the estimates of change and annual indices of abundance to a route regression analysis of SGS data. We also grouped SGS routes into Bird Conservation Regions (BCRs) and estimated population change and annual indices using BCRs within states and provinces as strata. Based on the hierarchical model–based estimates, we concluded that woodcock populations were declining in North America between 1968 and 2006 (trend = −0.9%/yr, 95% credible interval: −1.2, −0.5). Singing-Ground Survey results are generally similar between analytical approaches, but the hierarchical model has several important advantages over the route regression. Hierarchical models better accommodate changes in survey efficiency over time and space by treating strata, years, and observers as random effects in the context of a log-linear model, providing trend estimates that are derived directly from the annual indices. We also conducted a hierarchical model analysis of woodcock data from the Christmas Bird Count and the North American Breeding Bird Survey. All surveys showed general consistency in patterns of population change, but the SGS had the shortest credible intervals. We suggest that population management and conservation planning for woodcock involving interpretation of the SGS use estimates provided by the hierarchical model.