The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens

Testing optimality with experimental evolution: lysis time in a bacteriophage

Optimality models collapse the vagaries of genetics into simple trade-offs to calculate phenotypes expected to evolve by natural selection. Optimality approaches are commonly criticized for this neglect of genetic details, but resolution of this disagreement has been difficult. The importance of genetic details may be tested by experimental evolution of a trait for which an optimality model exists and in which genetic details can be studied. Here we evolved lysis time in bacteriophage T7, a virus of Escherichia coli. Lysis time is equivalent to the age of reproduction in an organism that reproduces once and then dies. Delaying lysis increases the number of offspring but slows generation time, and this trade-off renders the optimum sensitive to environmental conditions: earlier lysis is favored when bacterial hosts are dense, later lysis is favored when hosts are sparse. In experimental adaptations, T7 evolved close to the optimum in conditions favoring early lysis but not in conditions favoring late lysis. One of the late lysis adaptations exhibited no detectable phenotypic evolution despite genetic evolution; the other evolved only partly toward the expected optimum. Overall, the lysis time of the adapted phages remained closer to their starting values than predicted by the model. From the perspective of the optimality model, the experimental conditions were expected to select changes only along the postulated trade-off, but a trait outside the trade-off evolved as well. Evidence suggests that the model's failure ultimately stems from a violation of the trade-off, rather than a paucity of mutations.

Wrinkly-Spreader fitness in the two-dimensional agar plate microcosm: maladaptation, compensation and ecological success

Bacterial adaptation to new environments often leads to the establishment of new genotypes with significantly altered phenotypes. In the Wrinkly Spreader (WS), ecological success in static liquid microcosms was through the rapid colonisation of the air-liquid interface by the production of a cellulose-based biofilm. Rapid surface spreading was also seen on agar plates, but in this two-dimensional environment the WS appears maladapted and rapidly reverts to the ancestral smooth (SM)-like colony genotype. In this work, the fitness of WS relative to SM in mixed colonies was found to be low, confirming the WS instability on agar plates. By examining defined WS mutants, the maladaptive characteristic was found to be the expression of cellulose. SM-like revertants had a higher growth rate than WS and no longer expressed significant amounts of cellulose, further confirming that the expression of this high-cost polymer was the basis of maladaptation and the target of compensatory mutation in developing colonies. However, examination of the fate of WS-founded populations in either multiple-colony or single mega-colony agar plate microcosms demonstrated that the loss of WS lineages could be reduced under conditions in which the rapid spreading colony phenotype could dominate nutrient and oxygen access more effectively than competing SM/SM-like genotypes. WS-like isolates recovered from such populations showed increased WS phenotype stability as well as changes in the degree of colony spreading, confirming that the WS was adapting to the two-dimensional agar plate microcosm.

Pleiotropy and GAL pathway degeneration in yeast

Traits that do not contribute to fitness are expected to be lost during the course of evolution, either as a result of selection or drift. The Leloir pathway of galactose metabolism (GAL) is an extensively studied metabolic pathway that degenerated on at least three independent occasions during the evolutionary diversification of yeasts, suggesting that the pathway is costly to maintain in environments that lack galactose. Here I test this hypothesis by competing GAL pathway deletion mutants of Saccharomyces cerevisiae against an isogenic strain with an intact GAL pathway under conditions where expression of the pathway is normally induced, repressed, or uninduced. These experiments do not support the hypothesis that pleiotropy drives GAL pathway degeneration, because mutations that knock out individual GAL genes do not tend to increase fitness in the absence of galactose. At a molecular level, this result can be explained by the fact that yeast uses inexpensive regulatory proteins to tightly regulate the expression of structural genes that are costly to express. I argue that these results have general relevance for our understanding of the fitness consequences of gene disruption in yeast.

Populations under microevolutionary scrutiny: what will we gain?

Understanding the evolution of biodiversity and the function of biological systems are burning and linked questions in biology. Evolution of biodiversity begins at the level of microevolution, with the differentiation of individuals in populations. The study of this process splits into two conceptually different approaches (1) the concept of functional biology of testing hypothesis by precisely controlled and forward-directed experiments (digital and experimental evolution), and (2) the concept of a theory-based historical narrative (testing hypothesis on events in the past for their suitability to best explain the present). Here, I discuss and emphasize the benefits of the study of natural bacterial populations for a deeper understanding of prokaryotic biology. Also, I adress current problems in taxonomy at the 'species' level which obviously need discussion and clarification. I exemplify this with a natural model population for such studies, Bacillus simplex from "Evolution Canyon", Israel.

Population bottlenecks promote cooperation in bacterial biofilms

Population bottlenecks are assumed to play a key role in the maintenance of social traits in microbes. Ecological parameters such as colonisation or disturbances can favour cooperation through causing population bottlenecks that enhance genetic structuring (relatedness). However, the size of the population bottleneck is likely to play a crucial role in determining the success of cooperation. Relatedness is likely to increase with decreasing bottleneck size thus favouring the evolution of cooperation. I used an experimental evolution approach to test this prediction with biofilm formation by the bacterium Pseudomonas fluorescens as the cooperative trait. Replicate populations were exposed to disturbance events every four days under one of six population bottleneck treatments (from 10³ to 10⁸ bacterial cells). In line with predictions, the frequency of evolved cheats within the populations increased with increasing bottleneck size. This result highlights the importance of ecologically mediated population bottlenecks in the maintenance of social traits in microbes.

Experimental adaptation to high and low quality environments under different scales of temporal variation

We investigated the role of the scale of temporal variation in the evolution of generalism in populations of the bacterium Pseudomonas fluorescens. Replicate populations were propagated as batch cultures for approximately 1400 generations (192 days), in either high quality media only, low quality media only, or were alternated between the two at a range of temporal scales (between 1 and 48 days). Populations evolved in alternating media showed fitness increases in both media and the rate of alternation during selection had no effect on average fitness in either media. Moreover, the fitness of these populations in high quality media was the same as for populations evolved only in high quality media and likewise for low quality media. Populations evolved only in high or low quality media did not show fitness improvements in their nonselective media. These results indicate that cost-free generalists can evolve under a wide range of temporal variation.

Cooperation Peaks at Intermediate Disturbance

Explaining cooperation is a challenge for evolutionary biology. Surprisingly, the role of extrinsic ecological parameters remains largely unconsidered. Disturbances are widespread in nature and have evolutionary consequences. We develop a mathematical model predicting that cooperative traits most readily evolve at intermediate disturbance. Under infrequent disturbance, cooperation breaks down through the accumulation of evolved cheats. Higher rates of disturbance prevent this because the resulting bottlenecks increase genetic structuring (relatedness) promoting kin selection for cooperation. However, cooperation cannot be sustained under very frequent disturbance if population density remains below the level required for successful cooperation. We tested these predictions by using cooperative biofilm formation by the bacterium Pseudomonas fluorescens. The proportion of biofilm-forming bacteria peaked at intermediate disturbance, in a manner consistent with model predictions. Under infrequent and intermediate disturbance, most bacteria occupied the biofilm, but the proportion of cheats was higher under less frequent disturbance. Under frequent disturbance, many bacteria did not occupy the biofilm, suggesting that biofilm dwelling was not as beneficial under frequent versus intermediate disturbance. Given the ubiquity of disturbances in nature, these results suggest that they may play a major role in the evolution of social traits in microbes.

Evolutionary framework for protein sequence evolution and gene pleiotropy

In this article, we develop an evolutionary model for protein sequence evolution. Gene pleiotropy is characterized by K distinct but correlated components (molecular phenotypes) that affect the organismal fitness. These K molecular phenotypes are under stabilizing selection with microadaptation (SM) due to random optima shifts, the SM model. Random coding mutations generate a correlated distribution of K molecular phenotypes. Under this SM model, we further develop a statistical method to estimate the "effective" number of molecular phenotypes (K(e)) of the gene. Therefore, for the first time we can empirically evaluate gene pleiotropy from the protein sequence analysis. Case studies of vertebrate proteins indicate that K(e) is typically approximately 6-9. We demonstrate that the newly developed SM model of protein evolution may provide a basis for exploring genomic evolution and correlations.

The effects of competition and predation on diversification in a model adaptive radiation

Much of life's diversity is thought to have arisen through successive rounds of adaptive radiation-the rapid diversification of a lineage into a range of ecologically and phenotypically distinct species. Both resource competition and predation have been suggested as mechanisms driving this process, although the former is better studied than the latter. Here we show experimentally how predation by a protist, Tetrahymena thermophila, affects diversification in a model adaptive radiation of the bacterial prey, Pseudomonas fluorescens. We estimate the frequency-dependent fitness functions of competing niche-specialist prey in the presence and absence of predation, and use these to test hypotheses about the extent (measured as the number of new genotypes) and rate of diversification. Competition and predation independently generated diversifying selection that we show is capable of driving prey diversification to similar extents but at different rates, diversification being markedly delayed in the presence of predators. The cause of this delay stems from weaker diversifying selection due to the reduction in prey density caused by predation. Our results suggest that predation may play an under-appreciated role in driving adaptive radiations.

Niche occupation limits adaptive radiation in experimental microcosms

Adaptive radiations have played a key role in the evolution of biological diversity. The breadth of adaptive radiation in an invading lineage is likely to be influenced by the availability of ecological niches, which will be determined to some extent by the diversity of the resident community. High resident diversity may result in existing ecological niches being filled, inhibiting subsequent adaptive radiation. Conversely, high resident diversity could result in the creation of novel ecological niches or an increase in within niche competition driving niche partitioning, thus promoting subsequent diversification. We tested the role of resident diversity on adaptive radiations in experimental populations of the bacterium Pseudomonas fluorescens that readily diversify into a range of niche specialists when grown in a heterogeneous environment. We allowed an undiversified strain to invade resident communities that varied in the number of niche specialists. The breadth of adaptive radiation attainable by an invading lineage decreased with increasing niche occupation of the resident community. Our results highlight the importance of niche occupation as a constraint on adaptive radiation.

How does resource supply affect evolutionary diversification?

The availability of different resources in the environment can affect the outcomes of evolutionary diversification. A unimodal distribution of diversity with resource supply has been widely observed and explained previously in the context of selection acting in a spatially heterogeneous environment. Here, we propose an alternative mechanism to explain the relationship between resource supply and diversification that is based on selection for exploitation of different resources. To test this mechanism, we conducted a selection experiment using the bacterium Pseudomonas fluorescens in spatially homogeneous environments over a wide range of resource supply rates. Our results show that niche diversification peaks at intermediate levels of resource availability. We suggest that this unimodal relationship is due to evolutionary diversification that is driven by competition for resources but constrained by the ecological opportunity represented by different resource types. These processes may underlie some general patterns of diversity, including latitudinal gradients in species richness and the effects of anthropogenic enrichment of the environment.

Ecological Specialization and Adaptive Decay in Digital Organisms

The transition from generalist to specialist may entail the loss of unused traits or abilities, resulting in narrow niche breadth. Here we examine the process of specialization in digital organisms--self-replicating computer programs that mutate, adapt, and evolve. Digital organisms obtain energy by performing computations with numbers they input from their environment. We examined the evolutionary trajectory of generalist organisms in an ecologically narrow environment, where only a single computation yielded energy. We determined the extent to which improvements in this one function were associated with losses of other functions, leading to organisms that were highly specialized to perform only one or a few functions. Our results show that as organisms evolved improved performance of the selected function, they often lost the ability to perform other computations, and these losses resulted most often from the accumulation of neutral and deleterious mutations. Beneficial mutations, although relatively rare, were disproportionately likely to cause losses of function, indicating that antagonistic pleiotropy contributed significantly to niche breadth reductions in this system. Occasionally, unused functions were not lost and even increased in performance. Here we find that understanding how the functions were integrated into the genome was crucial to predictions of their maintenance.

Character displacement promotes cooperation in bacterial biofilms

Resource competition within a group of cooperators is expected to decrease selection for cooperative behavior but can also result in diversifying selection for the use of different resources, which in turn could retard the breakdown of cooperation. Diverse groups are likely to be less susceptible to invasion by noncooperating social cheats: First, competition repression resulting from character displacement may provide less of a selective advantage to cheating; second, cheats may trade off the ability to exploit cooperators that specialize in one type of resource against cooperators that specialize in another ; third, diverse communities of any kind may have higher invasion resistance because there are fewer resources available for an invader to use . Furthermore, diverse groups are likely to be more productive than clonal groups if a wider range of total resources are being used . We addressed these issues by using the cooperative trait of biofilm formation in Pseudomonas fluorescens. Character displacement through resource competition evolved within biofilms; productivity increased with increasing character displacement, and diverse biofilms were less susceptible to invasion by cheats. These results demonstrate that diversification into different ecological niches can minimize selection against cooperation in the face of local resource competition.

Increased susceptibility to repeated freeze-thaw cycles in Escherichia coli following long-term evolution in a benign environment

Background

In order to study the dynamics of evolutionary change, 12 populations of E. coli B were serially propagated for 20,000 generations in minimal glucose medium at constant 37°C. Correlated changes in various other traits have been previously associated with the improvement in competitive fitness in the selective environment. This study examines whether these evolved lines changed in their ability to tolerate the stresses of prolonged freezing and repeated freeze-thaw cycles during adaptation to a benign environment.

Results

All 12 lines that evolved in the benign environment for 20,000 generations are more sensitive to freeze-thaw cycles than their ancestor. The evolved lines have an average mortality rate of 54% per daily cycle, compared to the ancestral rate of 34%. By contrast, there was no significant difference between the evolved lines and their ancestor in mortality during prolonged freezing. There was also some variability among the evolved lines in susceptibility to repeated freeze-thaw cycles. Those lines that had evolved higher competitive fitness in the minimal glucose medium at 37°C also had higher mortality during freeze-thaw cycles. This variability was not associated, however, with differences among lines in DNA repair functionality and mutability.

Conclusion

The consistency of the evolutionary declines in freeze-thaw tolerance, the correlation between fitness in glucose medium at 37°C and mortality during freeze-thaw cycles, and the absence of greater declines in freeze-thaw survival among the hypermutable lines all indicate a trade-off between performance in minimal glucose medium at 37°C and the capacity to tolerate this stress. Analyses of the mutations that enhance fitness at 37°C may shed light on the physiological basis of this trade-off.

Cooperation: Integrating Evolutionary and Ecological Perspectives

Putting a competitive squeeze on a cooperative group has long been considered to encourage cheats. Now we learn that competition, by driving diversification among cooperators, can create groups that are both more productive and more resistant to defection.

Unraveling adaptive evolution: how a single point mutation affects the protein coregulation network

Understanding the mechanisms of evolution requires identification of the molecular basis of the multiple (pleiotropic) effects of specific adaptive mutations. We have characterized the pleiotropic effects on protein levels of an adaptive single-base pair substitution in the coding sequence of a signaling pathway gene in the bacterium Pseudomonas fluorescens SBW25. We find 52 proteomic changes, corresponding to 46 identified proteins. None of these proteins is required for the adaptive phenotype. Instead, many are found within specific metabolic pathways associated with fitness-reducing (that is, antagonistic) effects of the mutation. The affected proteins fall within a single coregulatory network. The mutation 'rewires' this network by drawing particular proteins into tighter coregulating relationships. Although these changes are specific to the mutation studied, the quantitatively altered proteins are also affected in a coordinated way in other examples of evolution to the same niche.

Adaptive radiation in microbial microcosms

It has often been argued that evolutionary diversification is the result of divergent natural selection for specialization on alternative resources. I provide a comprehensive review of experiments that examine the ecology and genetics of resource specialization and adaptive radiation in microbial microcosms. In these experiments, resource heterogeneity generates divergent selection for specialization on alternative resources. At a molecular level, the evolution of specialization is generally attributable to mutations that de-regulate the expression of existing biosynthetic and catabolic pathways. Trade-offs are associated with the evolution of resource specialization, but these trade-offs are often not the result of antagonistic pleiotropy. Replicate adaptive radiations result in the evolution of a similar assemblage of specialists, but the genetic basis of specialization differs in replicate radiations. The implications of microbial selection experiments for evolutionary theory are discussed and future directions of research are proposed.

Toward a molecular understanding of pleiotropy

Pleiotropy refers to the observation of a single gene influencing multiple phenotypic traits. Although pleiotropy is a common phenomenon with broad implications, its molecular basis is unclear. Using functional genomic data of the yeast Saccharomyces cerevisiae, here we show that, compared with genes of low pleiotropy, highly pleiotropic genes participate in more biological processes through distribution of the protein products in more cellular components and involvement in more protein-protein interactions. However, the two groups of genes do not differ in the number of molecular functions or the number of protein domains per gene. Thus, pleiotropy is generally caused by a single molecular function involved in multiple biological processes. We also provide genomewide evidence that the evolutionary conservation of genes and gene sequences positively correlates with the level of gene pleiotropy.

On The Necessity to Study Natural Bacterial Populations-The Model of Bacillus Simplex From "Evolution Canyons" I and II, Israel

How do bacteria evolve and speciate in natural environments? How does bacterial evolution relate to bacterial systematics? Exploring these answers is essential because bacteria profoundly impact life in general and, in particular, that of humans. Much insight into bacterial microevolution has come from theoretical and computational studies and from multigenerational laboratory systems ("Experimental Evolution"). These studies, however, do not take into account the diversity of modes of how bacteria can evolve under the complexity of the real world, i.e., nature. We argue, therefore, that for a comprehensive understanding of bacterial microevolution, it is essential to study natural populations. We underline our argument by introducing theBacillus simplexmodel from "Evolution Canyon", Israel. This metapopulation splits into different evolutionary lineages that have adapted to the microclimatically different slopes of "Evolution Canyon". It was shown that temperature stress is a major environmental factor driving theB. simplexadaptation and speciation progress. Therefore, this model population has proven highly suitable to study bacterial microevolution in natural habitats. Finally, we discuss theB. simplexintrapopulation divergence of lineages in light of current controversies on bacterial species concepts and taxon identification.

The Prerequisites for and Likelihood of Generalist‐Specialist Coexistence

Mathematical models of three-consumer-two-resource systems are used to explore the possibility of coexistence when one consumer is a generalist utilizing both resources, and the other two are specialists utilizing only one. Such coexistence requires strongly saturating functional or numerical responses in at least one consumer and the presence of sustained asynchronous variation in resource abundances. Given these conditions, the effects of three dichotomous factors on the range of parameters allowing coexistence are examined: flexible versus inflexible resource choice by the generalist, endogenous or exogenous cause of resource cycles, and location of the two resources in a single habitat versus two habitats. Coexistence of all three species is found to be possible for all combinations of these factors except for inflexible choice in a two-habitat environment. Generalists experience frequency-dependent fitness because, when they are abundant, they synchronize resource cycles and/or reduce their amplitude. When the generalist can adaptively adjust its relative foraging on the two resources, coexistence conditions are broadened considerably, and coexistence commonly occurs readily with exogenous variation in resource growth and with resources located in distinct habitats. Adaptive behavior increases the generalist's ability to both synchronize and dampen resource cycles.

Loss of dispensable genes is not adaptive in yeast

A substantial share of genes identified in yeast can be deleted without visible phenotypic effects. Current debate concentrates on the possible roles of seemingly dispensable genes. The costs of maintaining unnecessary functions has attracted little attention. The hypothesis of antagonistic pleiotropy postulates that adaptations to different constituents of the environment are likely to interfere with each other, and therefore loss of unnecessary functions is potentially advantageous. We tested an entire collection of nonessential yeast gene deletions in a benign and nutritionally rich environment in which the number of dispensable genes was particularly high. We applied a series of competition experiments that could detect differences in relative fitness of approximately 0.005. No beneficial deletions were found, except perhaps for the deletion of about a dozen genes that slightly improved competitive ability; however, a functional explanation of the fitness advantage is lacking. The paucity of beneficial gene deletions is striking because genetic adaptations to laboratory conditions are regularly observed in yeast. However, it accords with the finding that the gene contents of four species of Saccharomyces are nearly identical, despite up to 20 million years of independent evolution and extensive DNA sequence divergence. Such extreme conservation of functions would be improbable if there were periods of selection promoting the loss of temporarily dispensable genes. The evident cohesion of the yeast genomes may be their evolved feature or an intrinsic property of complex genetic systems.

Experimental evolution of Pseudomonas fluorescens in simple and complex environments

In complex environments that contain several substitutable resources, lineages may become specialized to consume only one or a few of them. Here we investigate the importance of environmental complexity in determining the evolution of niche width over approximately 900 generations in a chemically defined experimental system. We propagated 120 replicate lines of the bacterium Pseudomonas fluorescens in environments of different complexity by using between one and eight carbon substrates in each environment. Genotypes from populations selected in complex environments evolved greater mean and variance in fitness than those from populations selected in simple environments. Thus, lineages were able to adapt to several substrates simultaneously without any appreciable loss of function with respect to other substrates present in the media. There was greater genetic and genotype-by-environment interaction variance for fitness within populations selected in complex environments. It is likely that genetic variance in populations grown on complex media was maintained because the identity of the fittest genotype varied among carbon substrates. Our results suggest that evolution in complex environments will result neither in narrow specialists nor in complete generalists but instead in overlapping imperfect generalists, each of which has become adapted to a certain range of substrates but not to all.

Correlation of phenotype with the genotype of egg-contaminating Salmonella enterica serovar Enteritidis

The genotype of Salmonella enterica serovar Enteritidis was correlated with the phenotype using DNA-DNA microarray hybridization, ribotyping, and Phenotype MicroArray analysis to compare three strains that differed in colony morphology and phage type. No DNA hybridization differences were found between two phage type 13A (PT13A) strains that varied in biofilm formation; however, the ribotype patterns were different. Both PT13A strains had DNA sequences similar to that of bacteriophage Fels2, whereas the PT4 genome to which they were compared, as well as a PT4 field isolate, had a DNA sequence with some similarity to the bacteriophage ST64b sequence. Phenotype MicroArray analysis indicated that the two PT13A strains and the PT4 field isolate had similar respiratory activity profiles at 37 degrees C. However, the wild-type S. enterica serovar Enteritidis PT13A strain grew significantly better in 20% more of the 1,920 conditions tested when it was assayed at 25 degrees C than the biofilm-forming PT13A strain grew. Statistical analysis of the respiratory activity suggested that S. enterica serovar Enteritidis PT4 had a temperature-influenced dimorphic metabolism which at 25 degrees C somewhat resembled the profile of the biofilm-forming PT13A strain and that at 37 degrees C the metabolism was nearly identical to that of the wild-type PT13A strain. Although it is possible that lysogenic bacteriophage alter the balance of phage types on a farm either by lytic competition or by altering the metabolic processes of the host cell in subtle ways, the different physiologies of the S. enterica serovar Enteritidis strains correlated most closely with minor, rather than major, genomic changes. These results strongly suggest that the pandemic of egg-associated human salmonellosis that came into prominence in the 1980s is primarily an example of bacterial adaptive radiation that affects the safety of the food supply.

Promoters in the environment: transcriptional regulation in its natural context

Transcriptional activation of many bacterial promoters in their natural environment is not a simple on/off decision. The expression of cognate genes is integrated in layers of iterative regulatory networks that ensure the performance not only of the whole cell, but also of the bacterial population, and even the microbial community, in a changing environment. Unlike in vitro systems, where transcription initiation can be recreated with a handful of essential components, in vivo, promoters must process various physicochemical and metabolic signals to determine their output. This helps to achieve optimal bacterial fitness in extremely competitive niches. Promoters therefore merge specific responses to distinct signals with inclusive reactions to more general environmental changes.

The ecology and genetics of microbial diversity

Natural communities of microbes are often diverse, a fact that is difficult to reconcile with the action of natural selection in simple, uniform environments. We suggest that this apparent paradox may be resolved by considering the origin and fate of diversity in an explicitly ecological context. Here, we review insights into the ecological and genetic causes of diversity that stem from experiments with microbial populations evolving in the defined conditions of the laboratory environment. These studies highlight the importance of environmental structure in governing the fate of diversity and shed light on the genetic mechanisms generating diversity. We conclude by emphasizing the importance of placing detailed molecular-level studies within the context of a sound ecological and evolutionary framework.

Ecological constraints on diversification in a model adaptive radiation

Taxonomic diversification commonly occurs through adaptive radiation, the rapid evolution of a single lineage into a range of genotypes or species each adapted to a different ecological niche. Radiation size (measured as the number of new types) varies widely between phylogenetically distinct taxa and between replicate radiations within a single taxon where the ecological opportunities available seem to be identical. Here we show how variation in energy input (productivity) and environmental disturbance combine to determine the extent of diversification in a single radiating lineage of Pseudomonas fluorescens adapting to laboratory conditions. Diversity peaked at intermediate rates of both productivity and disturbance and declined towards the extremes in a manner reminiscent of well-known ecological patterns. The mechanism responsible for the decrease in diversity arises from pleiotropic fitness costs associated with niche specialization, the effects of which are modulated by gradients of productivity and disturbance. Our results indicate that ecological gradients may constrain the size of adaptive radiations, even in the presence of the strong diversifying selection associated with ecological opportunity, by decoupling evolutionary diversification from ecological coexistence.

Experimental adaptation of Salmonella typhimurium to mice

Experimental evolution is a powerful approach to study the dynamics and mechanisms of bacterial niche specialization. By serial passage in mice, we evolved 18 independent lineages of Salmonella typhimurium LT2 and examined the rate and extent of adaptation to a mainly reticuloendothelial host environment. Bacterial mutation rates and population sizes were varied by using wild-type and DNA repair-defective mutator (mutS) strains with normal and high mutation rates, respectively, and by varying the number of bacteria intraperitoneally injected into mice. After <200 generations of adaptation all lineages showed an increased fitness as measured by a faster growth rate in mice (selection coefficients 0.11-0.58). Using a generally applicable mathematical model we calculated the adaptive mutation rate for the wild-type bacterium to be >10(-6)/cell/generation, suggesting that the majority of adaptive mutations are not simple point mutations. For the mutator lineages, adaptation to mice was associated with a loss of fitness in secondary environments as seen by a reduced metabolic capability. During adaptation there was no indication that a high mutation rate was counterselected. These data show that S. typhimurium can rapidly and extensively increase its fitness in mice but this niche specialization is, at least in mutators, associated with a cost.