A SHIFT FROM MAGNITUDE TO SIGN EPISTASIS DURING ADAPTIVE EVOLUTION OF A BACTERIAL SOCIAL TRAIT

Although the importance of epistasis in evolution has long been recognized, remarkably little is known about the processes by which epistatic interactions evolve in real time in specific biological systems. Here, we have characterized how the epistatic fitness relationship between a social gene and an adapting genome changes radically over a short evolutionary time frame in the social bacterium Myxococcus xanthus. We show that a highly beneficial effect of this social gene in the ancestral genome is gradually reduced—and ultimately reversed into a deleterious effect—over the course of an experimental adaptive trajectory in which a primitive form of novel cooperation evolved. This reduction and reversal of a positive social allelic effect is driven solely by changes in the genetic context in which the gene is expressed as new mutations are sequentially fixed during adaptive evolution, and explicitly demonstrates a significant evolutionary change in the genetic architecture of an ecologically important social trait.     

Adaptation in Tunably Rugged Fitness Landscapes: The Rough Mount Fuji Model

Much of the current theory of adaptation is based on Gillespie’s mutational landscape model (MLM), which assumes that the fitness values of genotypes linked by single mutational steps are independent random variables. On the other hand, a growing body of empirical evidence shows that real fitness landscapes, while possessing a considerable amount of ruggedness, are smoother than predicted by the MLM. In the present article we propose and analyze a simple fitness landscape model with tunable ruggedness based on the rough Mount Fuji (RMF) model originally introduced by Aita et al. in the context of protein evolution. We provide a comprehensive collection of results pertaining to the topographical structure of RMF landscapes, including explicit formulas for the expected number of local fitness maxima, the location of the global peak, and the fitness correlation function. The statistics of single and multiple adaptive steps on the RMF landscape are explored mainly through simulations, and the results are compared to the known behavior in the MLM model. Finally, we show that the RMF model can explain the large number of second-step mutations observed on a highly fit first-step background in a recent evolution experiment with a microvirid bacteriophage.     

FISHER'S GEOMETRIC MODEL OF ADAPTATION MEETS THE FUNCTIONAL SYNTHESIS: DATA ON PAIRWISE EPISTASIS FOR FITNESS YIELDS INSIGHTS INTO THE SHAPE AND SIZE OF PHENOTYPE SPACE

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.     

ASYMMETRIC, BIMODAL TRADE-OFFS DURING ADAPTATION OF METHYLOBACTERIUM TO DISTINCT GROWTH SUBSTRATES

Trade-offs between selected and nonselected environments are often assumed to exist during adaptation. This phenomenon is prevalent in microbial metabolism, where many organisms have come to specialize on a narrow breadth of substrates. One well-studied example is methylotrophic bacteria that can use single-carbon (C₁) compounds as their sole source of carbon and energy, but generally use few, if any, multi-C compounds. Here, we use adaptation of experimental populations of the model methylotroph, Methylobacterium extorquens AM1, to C₁ (methanol) or multi-C (succinate) compounds to investigate specialization and trade-offs between these two metabolic lifestyles. We found a general trend toward trade-offs during adaptation to succinate, but this was neither universal nor showed a quantitative relationship with the extent of adaptation. After 1500 generations, succinate-evolved strains had a remarkably bimodal distribution of fitness values on methanol: either an improvement comparable to the strains adapted on methanol or the complete loss of the ability to grow on C₁ compounds. In contrast, adaptation to methanol resulted in no such trade-offs. Based on the substantial, asymmetric loss of C₁ growth during growth on succinate, we suggest that the long-term maintenance of C₁ metabolism across the genus Methylobacterium requires relatively frequent use of C₁ compounds to prevent rapid loss.     

LIFE-HISTORY CONSEQUENCES OF ADAPTATION TO LARVAL NUTRITIONAL STRESS IN DROSOPHILA

Many animal species face periods of chronic nutritional stress during which the individuals must continue to develop, grow, and/or reproduce despite low quantity or quality of food. Here, we use experimental evolution to study adaptation to such chronic nutritional stress in six replicate Drosophila melanogaster populations selected for the ability to survive and develop within a limited time on a very poor larval food. In unselected control populations, this poor food resulted in 20% lower egg‐to‐adult viability, 70% longer egg‐to‐adult development, and 50% lower adult body weight (compared to the standard food on which the flies were normally maintained). The evolutionary changes associated with adaptation to the poor food were assayed by comparing the selected and control lines in a common environment for different traits after 29–64 generations of selection. The selected populations evolved improved egg‐to‐adult viability and faster development on poor food. Even though the adult dry weight of selected flies when raised on the poor food was lower than that of controls, their average larval growth rate was higher. No differences in proportional pupal lipid content were observed. When raised on the standard food, the selected flies showed the same egg‐to‐adult viability and the same resistance to larval heat and cold shock as the controls and a slightly shorter developmental time. However, despite only 4% shorter development time, the adults of selected populations raised on the standard food were 13% smaller and showed 20% lower early‐life fecundity than the controls, with no differences in life span. The selected flies also turned out less tolerant to adult malnutrition. Thus, fruit flies have the genetic potential to adapt to poor larval food, with no detectable loss of larval performance on the standard food. However, adaptation to larval nutritional stress is associated with trade‐offs with adult fitness components, including adult tolerance to nutritional stress.     

ROLE OF SEX AND MIGRATION IN ADAPTATION TO SINK ENVIRONMENTS

Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single‐cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.     

EVOLUTIONARY RESCUE OF SEXUAL AND ASEXUAL POPULATIONS IN A DETERIORATING ENVIRONMENT

The environmental change experienced by many contemporary populations of organisms poses a serious risk to their survival. From the theory of evolutionary rescue, we predict that the combination of sex and genetic diversity should increase the probability of survival by increasing variation and thereby the probability of generating a type that can tolerate the stressful environment. We tested this prediction by comparing experimental populations of Chlamydomonas reinhardtii that differ in sexuality and in the initial amount of genetic diversity. The lines were serially propagated in an environment where the level of stress caused by salt increased over time from fresh water to the limits of marine conditions. In the long term, the combination of high diversity and obligate sexuality was most effective in supporting evolutionary rescue. Most of the adaptation to high‐salt environments in the obligate sexual‐high diversity lines had occurred by midway through the experiment, indicating that positive genetic correlations of adaptation to lethal stress with adaptation to sublethal stress greatly increased the probability of evolutionary rescue. The evolutionary rescue events observed in this study provide evidence that major shifts in ways of life can arise within short time frames through the action of natural selection in sexual populations.     

RATES OF FLORAL EVOLUTION: ADAPTATION TO BUMBLEBEE POLLINATION IN AN ALPINE WILDFLOWER,POLEMONIUM VISCOSUM

Animal pollinators are thought to shape floral evolution, yet the tempo of this process has seldom been measured. I used the prediction equation of quantitative genetics, R = h²S , to predict the rate at which a change in pollinator abundance may have caused divergence in floral morphology of the alpine skypilot, Polemonium viscosum. A selection experiment determined the rate at which such divergence can actually proceed. Corolla flare in this species increases by 12% from populations pollinated by a wide assemblage of insect visitors to those pollinated only by bumblebees. To simulate the evolutionary process giving rise to this change, I used a pollinator selection experiment. Plants with broad flowers set significantly more seeds than plants with narrow flowers under bumblebee pollination but had equivalent fecundity when visited by other insects or hand-pollinated. Bumblebee-mediated selection for broad corolla flare intensified from 0.07 at seed set to 0.17 at progeny establishment. Maternal parent-offspring regression yielded a confidence interval of 0.22–1.00 for trait heritability. Given these parameter estimates, the prediction equation shows that broadly flared flowers of bumblebee-pollinated P. viscosum could have evolved from narrower ones in a single generation. This prediction is matched by an observed 9% increase in offspring corolla flare after a single bout of bumblebee-mediated selection, relative to offspring of unselected controls. Findings show that plant populations can adapt rapidly to abrupt changes in pollinator assemblages.     

衣藻(Chlamydomonas sp)中间纤维及核纤层存在的证实(简报)

衣藻(Chlamydomonas sp)是属于绿藻门的最低等单细胞植物,为典型的真核生物。迄今以衣藻为材料所作的有关细胞骨架方面的研究多集中在微管蛋白(tubulin)。C.J.Miller等曾以衣藻(Chlamydomonas reinhardtii)全蛋白与几种中间纤维抗体进行免疫印迹实验有阳性反应,但是衣藻中是否存在中间纤维与核纤层是不清楚的问题。衣藻中间纤维与核纤层的形态研究更未见报道。目前认为中间纤维-核纤     

CHANGE OF UBIQUITINATED PROTEINS DURING THE CELL CYCLE IN CHLAMYDOMONAS (CHLOROPHYTA)1

Changes in the amount of heat shock-related ubiquitinated proteins in Chlamydomonas were investigated during the cell cycle and gamete induction. In a division-synchronized culture induced by periodic illumination, the amount of the 28-kDa ubiquitinated protein increased during the dark phase. This increase correlated with the increase of total DNA. Such an increase was repressed when nuclear DNA replication was inhibited with aphidicolin. These results suggest that ubiquitination to form the 28-kDa protein is involved in nuclear DNA replication or during the cell cycle. The amount of 31-kDa ubiquitinated protein gradually increased throughout the light phase and decreased in the dark phase. The amount of 28-kDa ubiquitinated protein also increased during gamete induction caused by nitrogen starvation, while that of the 31-kDa did not. These results suggest that the change of ubiquitination of 28-kDa protein mat play a fundamental role in the cell cycle and gamete induction in Chlamydomonas.     

ENVIRONMENT SPECIFIC PLEIOTROPY FACILITATES DIVERGENCE AT THE ECTODYSPLASIN LOCUS IN THREESPINE STICKLEBACK

Adaptive radiation occurs when divergent natural selection in different environments leads to phenotypic differentiation. The pleiotropic effects of underlying genes can either promote or constrain this diversification. Identifying the pleiotropic effects of genes responsible for divergent traits, and testing how the environment influences these effects, can therefore help to provide an understanding of how ecology drives evolutionary change between populations. Positive selection on low-armor alleles at the Ectodysplasin ( Eda ) locus in threespine stickleback has led to the repeated evolution of reduced armor in populations following freshwater colonization by fully armored marine sticklebacks. Here, we demonstrate that Eda has environmentally determined pleiotropic effects on armor and growth. When raised in freshwater, reduced armor sticklebacks carrying "low" alleles at Eda had increased growth rate relative to fully armored sticklebacks carrying "complete" alleles. In saltwater treatments this growth advantage was present during juvenile growth but lost during adult growth, suggesting that in this environment stickleback are able to develop full armor plates without sacrificing overall growth rate. The environment specific pleiotropic effects of Eda demonstrate that ecological factors can mediate the influence of genetic architecture in driving phenotypic evolution. Furthermore, because size is important for mate choice in stickleback, the growth rate differences influenced by Eda may have effects on reproductive isolation between marine and freshwater populations.     

EVOLUTIONARY ADAPTATION TO TEMPERATURE. V. ADAPTIVE MECHANISMS AND CORRELATED RESPONSES IN EXPERIMENTAL LINES OF ESCHERICHIA COLI

We previously demonstrated temperature-specific genetic adaptation in experimental lines of Escherichia coli. Six initially identical populations were propagated for 2000 generations under each of five regimes: constant 20°C, 32°C, 37°C, and 42°C, and a daily switch between 32°C and 42°C. Glucose was the sole carbon source in all cases. Here, we examine the physiological bases of adaptation to determine whether the same mechanisms evolved among the replicate lines within each thermal regime and across different regimes. Specifically, we investigate whether changes in glucose transport may account for the temperature-specific adaptation. We compared each line's direct response of fitness to glucose with its correlated response to maltose; glucose and maltose enter the cell by different pathways, but their catabolism is identical. Except for lines maintained at the ancestral temperature (37°C), almost all derived lines had significantly different fitnesses (relative to their common ancestor) in glucose and maltose, supporting the hypothesis that adaptation involved changes in glucose transport. An alternative explanation, that maltose transport decayed by genetic drift, appears unlikely for reasons that are discussed. Although most lines showed evidence of temperature-specific adaptation in glucose transport, several different mechanisms may underlie these improvements, as indicated by heterogeneity in correlated responses (across temperatures and substrates) among replicate lines adapted to the same regime. This heterogeneity provides a latent pool of genetic variation for responding to environmental change.     

GENETIC SIGNATURE OF ADAPTIVE PEAK SHIFT IN THREESPINE STICKLEBACK

Transition of an evolving population to a new adaptive optimum is predicted to leave a signature in the distribution of effect sizes of fixed mutations. If they affect many traits (are pleiotropic), large effect mutations should contribute more when a population evolves to a farther adaptive peak than to a nearer peak. We tested this prediction in wild threespine stickleback fish (Gasterosteus aculeatus) by comparing the estimated frequency of large effect genetic changes underlying evolution as the same ancestor adapted to two lake types since the end of the ice age. A higher frequency of large effect genetic changes (quantitative trait loci) contributed to adaptive evolution in populations that adapted to lakes representing a more distant optimum than to lakes in which the optimum phenotype was nearer to the ancestral state. Our results also indicate that pleiotropy, not just optimum overshoot, contributes to this difference. These results suggest that a series of adaptive improvements to a new environment leaves a detectable mark in the genome of wild populations. Although not all assumptions of the theory are likely met in natural systems, the prediction may be robust enough to the complexities of natural environments to be useful when forecasting adaptive responses to large environmental changes.     

THE EFFECTS OF POPULATION BOTTLENECKS ON CLONAL INTERFERENCE, AND THE ADAPTATION EFFECTIVE POPULATION SIZE

Clonal interference refers to the competition that arises in asexual populations when multiple beneficial mutations segregate simultaneously. A large body of theoretical and experimental work now addresses this issue. Although much of the experimental work is performed in populations that grow exponentially between periodic population bottlenecks, the theoretical work to date has addressed only populations of a constant size. We derive an analytical approximation for the rate of adaptation in the presence of both clonal interference and bottlenecks, and compare this prediction to the results of an individual-based simulation, showing excellent agreement in the parameter regime in which clonal interference prevails. We also derive an appropriate definition for the effective population size for adaptive evolution experiments in the presence of population bottlenecks. This "adaptation effective population size" allows for a good approximation of the expected rate of adaptation, either in the strong-selection weak-mutation regime, or when clonal interference comes into play. In the multiple mutation regime, when the product of the population size and mutation rate is extremely large, these results no longer hold.     

Pervasive,yet idiosyncratic,epistatic pleiotropy during adaptation in a behaviourally complex microbe

Understanding how multiple mutations interact to jointly impact multiple ecologically important traits is critical for creating a robust picture of organismal fitness and the process of adaptation. However, this is complicated by both environmental heterogeneity and the complexity of genotype‐to‐phenotype relationships generated by pleiotropy and epistasis. Moreover, little is known about how pleiotropic and epistatic relationships themselves change over evolutionary time. The soil bacterium Myxococcus xanthus employs several distinct social traits across a range of environments. Here, we use an experimental lineage of M. xanthus that evolved a novel form of social motility to address how interactions between epistasis and pleiotropy evolve. Specifically, we test how mutations accumulated during selection on soft agar pleiotropically affect several other social traits (hard agar motility, predation and spore production). Relationships between changes in swarming rate in the selective environment and the four other traits varied greatly over time in both direction and magnitude, both across timescales of the entire evolutionary lineage and individual evolutionary time steps. We also tested how a previously defined epistatic interaction is pleiotropically expressed across these traits. We found that phenotypic effects of this epistatic interaction were highly correlated between soft and hard agar motility, but were uncorrelated between soft agar motility and predation, and inversely correlated between soft agar motility and spore production. Our results show that ‘epistatic pleiotropy’ varied greatly in magnitude, and often even in sign, across traits and over time, highlighting the necessity of simultaneously considering the interacting complexities of pleiotropy and epistasis when studying the process of adaptation.     

FUNCTIONAL GENETIC DIVERGENCE IN HIGH CO2 ADAPTED EMILIANIA HUXLEYI POPULATIONS

Predicting the impacts of environmental change on marine organisms, food webs, and biogeochemical cycles presently relies almost exclusively on short‐term physiological studies, while the possibility of adaptive evolution is often ignored. Here, we assess adaptive evolution in the coccolithophore Emiliania huxleyi, a well‐established model species in biological oceanography, in response to ocean acidification. We previously demonstrated that this globally important marine phytoplankton species adapts within 500 generations to elevated CO₂. After 750 and 1000 generations, no further fitness increase occurred, and we observed phenotypic convergence between replicate populations. We then exposed adapted populations to two novel environments to investigate whether or not the underlying basis for high CO₂‐adaptation involves functional genetic divergence, assuming that different novel mutations become apparent via divergent pleiotropic effects. The novel environment “high light” did not reveal such genetic divergence whereas growth in a low‐salinity environment revealed strong pleiotropic effects in high CO₂ adapted populations, indicating divergent genetic bases for adaptation to high CO₂. This suggests that pleiotropy plays an important role in adaptation of natural E. huxleyi populations to ocean acidification. Our study highlights the potential mutual benefits for oceanography and evolutionary biology of using ecologically important marine phytoplankton for microbial evolution experiments.     

SHIFTING FITNESS LANDSCAPES IN RESPONSE TO ALTERED ENVIRONMENTS

The role of adaptation in molecular evolution has been contentious for decades. Here, we shed light on the adaptive potential in Saccharomyces cerevisiae by presenting systematic fitness measurements for all possible point mutations in a region of Hsp90 under four environmental conditions. Under elevated salinity, we observe numerous beneficial mutations with growth advantages up to 7% relative to the wild type. All of these beneficial mutations were observed to be associated with high costs of adaptation. We thus demonstrate that an essential protein can harbor adaptive potential upon an environmental challenge, and report a remarkable fit of the data to a version of Fisher's geometric model that focuses on the fitness trade‐offs between mutations in different environments.     

ADAPTATION RATES OF LYTIC VIRUSES DEPEND CRITICALLY ON WHETHER HOST CELLS SURVIVE THE BOTTLENECK

We use a branching process approach to estimate the substitution rate, the rate at which beneficial mutations occur and fix, in populations of lytic viruses whose growth is controlled by periodic population bottlenecks. Our model predicts that substitution rates, and by extension adaptation rates, are profoundly affected by the survival of infected host cells at the bottleneck. In particular, we find that direct transfer (or environmental) bottlenecks, in which some fraction of both free virus and host cells are preserved, are associated with relatively slow adaptation rates for the virus. In contrast, viruses can adapt much more quickly when only free virus is transferred to a new host population, as is typical in an epidemiological setting. Finally, when premature lysis of the host‐cell population is induced at the bottleneck, we predict that adaptation rates for the virus will, in general, be faster still. These results hold irrespective of the life‐history trait affected by the beneficial mutation. The substitution rates in the presence of environmental bottlenecks are predicted to be as much as an order of magnitude lower than in the other two cases.     

LOCALIZATION OF OXYTETRACYCLINE IN CHLAMYDOMONAS REINHARDTII (CHLOROPHYCEAE)1

Oxytetracycline (OTC) is an important antimicrobial used in aquaculture. However, residues of OTC have been isolated from nontarget aquatic organisms, sediments, and water located near aquaculture facilities. Identifying OTC in plant material is particularly difficult due to interference from pigments and polyphenol substances but is important especially for algae since they are a primary food source for fish in early life stages. In this study, we describe the effect of OTC (0.1, 1, 10, 25, 50, 100 μg · mL^?1) on cell growth, and the localization of OTC (0, 1, 25, 100 μg · mL^?1) in vacuoles of Chlamydomonas reinhardtii P. A. Dang. (wildtype, ATCC 18798). We also present a method for semiquantifying OTC in living cells using fluorescent microscopy and Adobe Photoshop. We exposed algal cells to OTC and sampled after 2 or 7 d exposure. On day 7, OTC significantly inhibited algal growth at 1, 10, 25, 50, and 100 μg · mL^?1. When viewed with fluorescent microscopy, cells exposed to the 25 and 100 μg · mL^?1 contained yellow fluorescent areas, ≤1 μm in diameter that were easily discernable against the red fluorescence of the intracellular chl. The fluorescent areas corresponded to small spherical vacuoles (i.e., polyphosphate bodies that contain calcium and magnesium complexed with polyphosphate) seen in the cells by LM. Since OTC has a high affinity for divalent cations, we suggest that OTC is localized in these vacuoles.