共查询到20条相似文献,搜索用时 15 毫秒
1.
Mats E. Pettersson Ronald M. Nelson Örjan Carlborg 《Evolution; international journal of organic evolution》2012,66(12):3945-3949
Simulations on a model system where a variance‐controlling master locus scales the effects of a set of effector loci show that selection affects the variance‐controlling locus more strongly than the effector loci, and that the direction of selection is dependent on the frequency of environmental changes. 相似文献
2.
When multiple substitutions affect a trait in opposing ways, they are often assumed to be compensatory, not only with respect to the trait, but also with respect to fitness. This type of compensatory evolution has been suggested to underlie the evolution of protein structures and interactions, RNA secondary structures, and gene regulatory modules and networks. The possibility for compensatory evolution results from epistasis. Yet if epistasis is widespread, then it is also possible that the opposing substitutions are individually adaptive. I term this possibility an adaptive reversal. Although possible for arbitrary phenotype‐fitness mappings, it has not yet been investigated whether such epistasis is prevalent in a biologically realistic setting. I investigate a particular regulatory circuit, the type I coherent feed‐forward loop, which is ubiquitous in natural systems and is accurately described by a simple mathematical model. I show that such reversals are common during adaptive evolution, can result solely from the topology of the fitness landscape, and can occur even when adaptation follows a modest environmental change and the network was well adapted to the original environment. The possibility of adaptive reversals warrants a systems perspective when interpreting substitution patterns in gene regulatory networks. 相似文献
3.
Jeremy A. Draghi Joshua B. Plotkin 《Evolution; international journal of organic evolution》2013,67(11):3120-3131
The contribution to an organism's phenotype from one genetic locus may depend upon the status of other loci. Such epistatic interactions among loci are now recognized as fundamental to shaping the process of adaptation in evolving populations. Although little is known about the structure of epistasis in most organisms, recent experiments with bacterial populations have concluded that antagonistic interactions abound and tend to deaccelerate the pace of adaptation over time. Here, we use the NK model of fitness landscapes to examine how natural selection biases the mutations that substitute during evolution based on their epistatic interactions. We find that, even when beneficial mutations are rare, these biases are strong and change substantially throughout the course of adaptation. In particular, epistasis is less prevalent than the neutral expectation early in adaptation and much more prevalent later, with a concomitant shift from predominantly antagonistic interactions early in adaptation to synergistic and sign epistasis later in adaptation. We observe the same patterns when reanalyzing data from a recent microbial evolution experiment. These results show that when the order of substitutions is not known, standard methods of analysis may suggest that epistasis retards adaptation when in fact it accelerates it. 相似文献
4.
Daniel M. Weinreich Jennifer L. Knies 《Evolution; international journal of organic evolution》2013,67(10):2957-2972
The functional synthesis uses experimental methods from molecular biology, biochemistry and structural biology to decompose evolutionarily important mutations into their more proximal mechanistic determinants. However these methods are technically challenging and expensive. Noting strong formal parallels between R.A. Fisher's geometric model of adaptation and a recent model for the phenotypic basis of protein evolution, we sought to use the former to make inferences into the latter using data on pairwise fitness epistasis between mutations. We present an analytic framework for classifying pairs of mutations with respect to similarity of underlying mechanism on this basis, and also show that these data can yield an estimate of the number of mutationally labile phenotypes underlying fitness effects. We use computer simulations to explore the robustness of our approach to violations of analytic assumptions and analyze several recently published datasets. This work provides a theoretical complement to the functional synthesis as well as a novel test of Fisher's geometric model. 相似文献
5.
Joel R. Peck David Waxman 《Evolution; international journal of organic evolution》2010,64(11):3300-3309
The earliest organisms are thought to have had high mutation rates. It has been asserted that these high mutation rates would have severely limited the information content of early genomes. This has led to a well‐known “paradox” because, in contemporary organisms, the mechanisms that suppress mutations are quite complex and a substantial amount of information is required to construct these mechanisms. The paradox arises because it is not clear how efficient error‐suppressing mechanisms could have evolved, and thus allowed the evolution of complex organisms, at a time when mutation rates were too high to permit the maintenance of very substantial amounts of information within genomes. Here, we use concepts from the formal theory of information to calculate the amount of genomic information that can be maintained. We identify conditions under which much higher levels of genomic information can be maintained than previously considered possible among origin‐of‐life researchers. In particular, we find that the highest levels of information are maintained when many genotypes produce identical phenotypes, and when reproduction occasionally involves recombination between multiple parental genomes. There is a good reason to believe that these conditions are relevant for very early organisms, and thus the results presented may provide a solution to a long‐standing logical problem associated with the early evolution of life. 相似文献
6.
Natural populations must constantly adapt to ever‐changing environmental conditions. A particularly interesting question is whether such adaptations can be reversed by returning the population to an ancestral environment. Such evolutionary reversals have been observed in both natural and laboratory populations. However, the factors that determine the reversibility of evolution are still under debate. The time scales of environmental change vary over a wide range, but little is known about how the rate of environmental change influences the reversibility of evolution. Here, we demonstrate computationally that slowly switching between environments increases the reversibility of evolution for small populations that are subject to only modest clonal interference. For small populations, slow switching reduces the mean number of mutations acquired in a new environment and also increases the probability of reverse evolution at each of these “genetic distances.” As the population size increases, slow switching no longer reduces the genetic distance, thus decreasing the evolutionary reversibility. We confirm this effect using both a phenomenological model of clonal interference and also a Wright–Fisher stochastic simulation that incorporates genetic diversity. Our results suggest that the rate of environmental change is a key determinant of the reversibility of evolution, and provides testable hypotheses for experimental evolution. 相似文献
7.
Florence Bansept Loïc Marrec Anne‐Florence Bitbol Claude Loverdo 《Evolution; international journal of organic evolution》2019,73(6):1077-1088
The body is home to a diverse microbiota, mainly in the gut. Resistant bacteria are selected by antibiotic treatments, and once resistance becomes widespread in a population of hosts, antibiotics become useless. Here, we develop a multiscale model of the interaction between antibiotic use and resistance spread in a host population, focusing on an important aspect of within‐host immunity. Antibodies secreted in the gut enchain bacteria upon division, yielding clonal clusters of bacteria. We demonstrate that immunity‐driven bacteria clustering can hinder the spread of a novel resistant bacterial strain in a host population. We quantify this effect both in the case where resistance preexists and in the case where acquiring a new resistance mutation is necessary for the bacteria to spread. We further show that the reduction of spread by clustering can be countered when immune hosts are silent carriers, and are less likely to get treated, and/or have more contacts. We demonstrate the robustness of our findings to including stochastic within‐host bacterial growth, a fitness cost of resistance, and its compensation. Our results highlight the importance of interactions between immunity and the spread of antibiotic resistance, and argue in the favor of vaccine‐based strategies to combat antibiotic resistance. 相似文献
8.
Claude Loverdo James O. Lloyd‐Smith 《Evolution; international journal of organic evolution》2013,67(6):1815-1822
Viral particles (virions) are made of genomic material packaged with proteins, drawn from the pool of proteins in the parent cell. It is well known that when virion concentrations are high, cells can be coinfected with multiple viral strains that can complement each other. Viral genomes can then interact with proteins derived from different strains, in a phenomenon known as phenotypic mixing. But phenotypic mixing is actually far more common: viruses mutate very often, and each time a mutation occurs, the parent cell contains different types of viral genomes. Due to phenotypic mixing, changes in viral phenotypes can be shifted by a generation from the mutations that cause them. In the regime of evolutionary invasion and escape, when mutations are crucial for the virus to survive, this timing can have a large influence on the probability of emergence of an adapted strain. Modeling the dynamics of viral evolution in these contexts thus requires attention to the mutational mechanism and the determinants of fitness. 相似文献
9.
Michel Durinx Tom J. M. Van Dooren 《Evolution; international journal of organic evolution》2009,63(2):334-352
In genetic polymorphisms of two alleles, heterozygous individuals may contribute to the next generation on average more or fewer descendants than the homozygotes. Two different evolutionary responses that remove a disadvantageous heterozygote phenotype from the population are the evolution of strictly assortative mate choice, and that of a modifier making one of the two alleles completely dominant. We derive invasion fitness of mutants introducing dominance or assortative mate choice in a randomly mating population with a genetic polymorphism for an ecological trait. Mutations with small effects as well as mutants introducing complete dominance or perfect assorting are considered. Using adaptive dynamics techniques, we are able to calculate the ratio of fitness gradients for the effects of a dominance modifier and a mate choice locus, near evolutionary branching points. With equal resident allele frequencies, selection for mate choice is always stronger. Dominance is more strongly selected than assortative mating when the resident (common) alleles have very unequal frequencies at equilibrium. With female mate choice the difference in frequencies where dominance is more strongly selected is smaller than when mutants of both sexes can choose without costs. A symmetric resource-competition model illustrates the results. 相似文献
10.
Brandon M. Invergo Ludovica Montanucci Jaume Bertranpetit 《Proceedings. Biological sciences / The Royal Society》2015,282(1820)
Determining the influence of complex, molecular-system dynamics on the evolution of proteins is hindered by the significant challenge of quantifying the control exerted by the proteins on system output. We have employed a combination of systems biology and molecular evolution analyses in a first attempt to unravel this relationship. We employed a comprehensive mathematical model of mammalian phototransduction to predict the degree of influence that each protein in the system exerts on the high-level dynamic behaviour. We found that the genes encoding the most dynamically sensitive proteins exhibit relatively relaxed evolutionary constraint. We also investigated the evolutionary and epistatic influences of the many nonlinear interactions between proteins in the system and found several pairs to have coevolved, including those whose interactions are purely dynamical with respect to system output. This evidence points to a key role played by nonlinear system dynamics in influencing patterns of molecular evolution. 相似文献
11.
Westneat DF 《Evolution; international journal of organic evolution》2012,66(3):890-895
Social interactions have a powerful effect on the evolutionary process. Recent attempts to synthesize models of social selection with equations for indirect genetic effects (McGlothlin et al. 2010) provide a broad theoretical base from which to study selection and evolutionary response in the context of social interactions. However, this framework concludes that social selection will lead to evolution only if the traits carried by social partners are nonrandomly associated. I suggest this conclusion is incomplete, and that traits that do not covary between social partners can nevertheless lead to evolution via interactive effects on fitness. Such effects occur when there are functional interactions between traits, and as an example I use the interplay in water striders (Gerridae) between grasping appendages carried by males and spines by females. Functional interactive effects between traits can be incorporated into both the equations for social selection and the general model of social evolution proposed by McGlothlin et al. These expanded equations would accommodate adaptive coevolution in social interactions, integrate the quantitative genetic approach to social evolution with game theoretical approaches, and stimulate some new questions about the process of social evolution. 相似文献
12.
Gregor Rolshausen Shahin Muttalib Renaud Kaeuffer Krista B. Oke Dieta Hanson Andrew P. Hendry 《Evolution; international journal of organic evolution》2015,69(9):2289-2302
Populations receiving high maladaptive gene flow are expected to experience strong directional selection—because gene flow pulls mean phenotypes away from local fitness peaks. We tested this prediction by means of a large and replicated mark‐recapture study of threespine stickleback (Gasterosteus aculeatus) in two stream populations. One of the populations (outlet) experiences high gene flow from the lake population and its morphology is correspondingly poorly adapted. The other population (inlet) experiences very low gene flow from the lake population and its morphology is correspondingly well adapted. Contrary to the above prediction, selection was not stronger in the outlet than in the inlet, a result that forced us to consider potential reasons for why maladaptive gene flow might not increase selection. Of particular interest, we show by means of a simple population genetic model that maladaptive gene flow can—under reasonable conditions—decrease the strength of directional selection. This outcome occurs when immigrants decrease mean fitness in the resident population, which decreases the strength of selection against maladapted phenotypes. We argue that this previously unrecognized effect of gene flow deserves further attention in theoretical and empirical studies. 相似文献
13.
Sarah P. Hammarlund Brian D. Connelly Katherine J. Dickinson Benjamin Kerr 《Evolution; international journal of organic evolution》2016,70(6):1376-1385
The evolution of cooperation—costly behavior that benefits others—faces one clear obstacle. Namely, cooperators are always at a competitive disadvantage relative to defectors, individuals that reap the benefits, but evade the cost of cooperation. One solution to this problem involves genetic hitchhiking, where the allele encoding cooperation becomes linked to a beneficial mutation, allowing cooperation to rise in abundance. Here, we explore hitchhiking in the context of adaptation to a stressful environment by cooperators and defectors with spatially limited dispersal. Under such conditions, clustered cooperators reach higher local densities, thereby experiencing more mutational opportunities than defectors. Thus, the allele encoding cooperation has a greater probability of hitchhiking with alleles conferring stress adaptation. We label this probabilistic enhancement the “Hankshaw effect” after the character Sissy Hankshaw, whose anomalously large thumbs made her a singularly effective hitchhiker. Using an agent‐based model, we reveal a broad set of conditions that allow the evolution of cooperation through this effect. Additionally, we show that spite, a costly behavior that harms others, can evolve by the Hankshaw effect. While in an unchanging environment these costly social behaviors have transient success, in a dynamic environment, cooperation and spite can persist indefinitely. 相似文献
14.
Ace North Juho Pennanen Otso Ovaskainen Anna‐Liisa Laine 《Evolution; international journal of organic evolution》2011,65(1):79-89
In spatially heterogeneous environments, the processes of gene flow, mutation, and sexual reproduction generate local genetic variation and thus provide material for local adaptation. On the other hand, these processes interchange maladapted for adapted genes and so, in each case, the net influence may be to reduce local adaptation. Previous work has indicated that this is the case in stable populations, yet it is less clear how the factors play out during population growth, and in the face of temporal environmental stochasticity. We address this issue with a spatially explicit, stochastic model. We find that dispersal, mutation, and sexual reproduction can all accelerate local adaptation in growing populations, although their respective roles may depend on the genetic make‐up of the founding population. All three processes reduce local adaptation, however, in the long term, that is when population growth becomes balanced by density‐dependent competition. These relationships are qualitatively maintained, although quantitatively reduced, if the resources are locally ephemeral. Our results suggest that species with high levels of local adaptation within their ranges may not be the same species that harbor potential for rapid local adaptation during population expansion. 相似文献
15.
Sebastian Matuszewski Joachim Hermisson Michael Kopp 《Evolution; international journal of organic evolution》2014,68(9):2571-2588
Fisher's geometric model has been widely used to study the effects of pleiotropy and organismic complexity on phenotypic adaptation. Here, we study a version of Fisher's model in which a population adapts to a gradually moving optimum. Key parameters are the rate of environmental change, the dimensionality of phenotype space, and the patterns of mutational and selectional correlations. We focus on the distribution of adaptive substitutions, that is, the multivariate distribution of the phenotypic effects of fixed beneficial mutations. Our main results are based on an “adaptive‐walk approximation,” which is checked against individual‐based simulations. We find that (1) the distribution of adaptive substitutions is strongly affected by the ecological dynamics and largely depends on a single composite parameter γ, which scales the rate of environmental change by the “adaptive potential” of the population; (2) the distribution of adaptive substitution reflects the shape of the fitness landscape if the environment changes slowly, whereas it mirrors the distribution of new mutations if the environment changes fast; (3) in contrast to classical models of adaptation assuming a constant optimum, with a moving optimum, more complex organisms evolve via larger adaptive steps. 相似文献
16.
Wei‐Hsiang Lin Mark J. Rocco Amelia Bertozzi‐Villa Edo Kussell 《Evolution; international journal of organic evolution》2015,69(6):1448-1460
Populations can adapt to changing environments by using allelic diversity, yet whether diversity is recently derived or ancestral is often debated. Although evolution could productively use both types of diversity in a changing environment, their relative frequency has not been quantified. We address this question experimentally using budding yeast strains that harbor a tandem repeat containing URA3 gene, which we expose to cyclical selection and counterselection. We characterize and quantify the dynamics of frameshift events in the URA3 gene in eight populations over 12 cycles of selection and find that ancestral alleles account for 10–20% of all adaptive events. Using a general model of fluctuating selection, we determine how these results depend on mutation rates, population sizes, and fluctuation timescales. We quantify the contribution of derived alleles to the adaptation process using the de novo mutation rate along the population's ancestral lineage, a novel measure that is applicable in a wide range of settings. We find that the adaptive dynamics undergoes a sharp transition from selection on ancestral alleles to selection on derived alleles as fluctuation timescales increase. Our results demonstrate that fluctuations can select between different modes of adaptation over evolutionary timescales. 相似文献
17.
Tim Connallon Matthew D. Hall 《Evolution; international journal of organic evolution》2016,70(10):2186-2198
Females and males have conflicting evolutionary interests. Selection favors the evolution of different phenotypes within each sex, yet divergence between the sexes is constrained by the shared genetic basis of female and male traits. Current theory predicts that such “sexual antagonism” should be common: manifesting rapidly during the process of adaptation, and slow in its resolution. However, these predictions apply in temporally stable environments. Environmental change has been shown empirically to realign the direction of selection acting on shared traits and thereby alleviate signals of sexually antagonistic selection. Yet there remains no theory for how common sexual antagonism should be in changing environments. Here, we analyze models of sex‐specific evolutionary divergence under directional and cyclic environmental change, and consider the impact of genetic correlations on long‐run patterns of sex‐specific adaptation. We find that environmental change often aligns directional selection between the sexes, even when they have divergent phenotypic optima. Nevertheless, some forms of environmental change generate persistent sexually antagonistic selection that is difficult to resolve. Our results reinforce recent empirical observations that changing environmental conditions alleviate conflict between males and females. They also generate new predictions regarding the scope for sexually antagonistic selection and its resolution in changing environments. 相似文献
18.
K. Petren 《Evolution; international journal of organic evolution》2013,67(12):3383-3385
The main objective of this special section is not to review the broad field of landscape genetics, but to provide a glimpse of how the developing landscape genetics perspective has the potential to change the way we study evolution. Evolutionary landscape genetics is the study of how migration and population structure affects evolutionary processes. As a field it dates back to Sewall Wright and the origin of theoretical population genetics, but empirical tests of adaptive processes of evolution in natural landscapes have been rare. Now, with recent developments in technology, methodology, and modeling tools, we are poised to trace adaptive genetic variation across space and through time. Not only will we see more empirical tests of classical theory, we can expect to see new phenomena emerging, as we reveal complex interactions among evolutionary processes as they unfold in natural landscapes. 相似文献
19.
Brent E. Allman Daniel B. Weissman 《Evolution; international journal of organic evolution》2018,72(4):722-734
Selective sweeps reduce neutral genetic diversity. In sexual populations, this “hitchhiking” effect is thought to be limited to the local genomic region of the sweeping allele. While this is true in panmictic populations, we find that in spatially extended populations the combined effects of many unlinked sweeps can affect patterns of ancestry (and therefore neutral genetic diversity) across the whole genome. Even low rates of sweeps can be enough to skew the spatial locations of ancestors such that neutral mutations that occur in an individual living outside a small region in the center of the range have virtually no chance of fixing in the population. The fact that nearly all ancestry rapidly traces back to a small spatial region also means that relatedness between individuals falls off very slowly as a function of the spatial distance between them. 相似文献
20.
Guillaume Martin Thomas Lenormand 《Evolution; international journal of organic evolution》2015,69(6):1433-1447
When are mutations beneficial in one environment and deleterious in another? More generally, what is the relationship between mutation effects across environments? These questions are crucial to predict adaptation in heterogeneous conditions in a broad sense. Empirical evidence documents various patterns of fitness effects across environments but we still lack a framework to analyze these multivariate data. In this article, we extend Fisher's geometrical model to multiple environments determining distinct peaks. We derive the fitness distribution, in one environment, among mutants with a given fitness in another and the bivariate distribution of random mutants’ fitnesses across two or more environments. The geometry of the phenotype‐fitness landscape is naturally interpreted in terms of fitness trade‐offs between environments. These results may be used to fit/predict empirical distributions or to predict the pattern of adaptation across heterogeneous conditions. As an example, we derive the genomic rate of substitution and of adaptation in a metapopulation divided into two distinct habitats in a high migration regime and show that they depend critically on the geometry of the phenotype‐fitness landscape. 相似文献