Mutational collapse of fitness in marginal habitats and the evolution of ecological specialisation

In spatially heterogeneous environments, natural selection for maintenance of adaptation to habitats that contribute little to the population's reproduction is weak. In this paper we model a mechanism that can result in loss of fitness in such marginal habitats, and thus lead to specialisation on the main habitat. It involves accumulation of mutations that are deleterious in the marginal habitat but neutral or nearly so in the main habitat (mutations deleterious in the main habitat and neutral in the marginal habitat have a negligible influence). If the contribution of the marginal habitat to total reproduction in the absence of the mutations is less than a threshold value, selection is too weak to counter accumulation of such mutations. A positive feedback then results in loss of fitness in the marginal habitat. This mechanism does not require antagonistic pleiotropy in adaptation to different habitats, although antagonistic pleiotropy facilitates the mutational collapse of fitness in the marginal habitat. We suggest that deleterious mutations with habitat-specific expression may play a role in the evolution of ecological specialisation and promote evolutionary conservatism of ecological niches.     

The Environment Affects Epistatic Interactions to Alter the Topology of an Empirical Fitness Landscape

The fitness effect of mutations can be influenced by their interactions with the environment, other mutations, or both. Previously, we constructed 32 ( = 2⁵) genotypes that comprise all possible combinations of the first five beneficial mutations to fix in a laboratory-evolved population of Escherichia coli. We found that (i) all five mutations were beneficial for the background on which they occurred; (ii) interactions between mutations drove a diminishing returns type epistasis, whereby epistasis became increasingly antagonistic as the expected fitness of a genotype increased; and (iii) the adaptive landscape revealed by the mutation combinations was smooth, having a single global fitness peak. Here we examine how the environment influences epistasis by determining the interactions between the same mutations in two alternative environments, selected from among 1,920 screened environments, that produced the largest increase or decrease in fitness of the most derived genotype. Some general features of the interactions were consistent: mutations tended to remain beneficial and the overall pattern of epistasis was of diminishing returns. Other features depended on the environment; in particular, several mutations were deleterious when added to specific genotypes, indicating the presence of antagonistic interactions that were absent in the original selection environment. Antagonism was not caused by consistent pleiotropic effects of individual mutations but rather by changing interactions between mutations. Our results demonstrate that understanding adaptation in changing environments will require consideration of the combined effect of epistasis and pleiotropy across environments.     

Gene-flow between niches facilitates local adaptation in sexual populations

In sexual populations, gene-flow between niches is predicted to have differential consequences on local adaptation contingent upon the nature of trade-offs underlying local adaptation. Sex retards local adaptation if antagonistic pleiotropy underlies trade-offs, but facilitates adaptation if mutation accumulation underlies trade-offs. We evaluate the effect of sex in heterogeneous environments by manipulating gene-flow between two niches in sexual and asexual populations using steady-state microcosm experiments with yeast. We find that only sex in the presence of gene-flow promotes simultaneous local adaptation to different niches, presumably as this exposes mutations neutrally accrued in alternate niches to selection. This finding aligns with work showing mutation accumulation underlies trade-offs to local adaptation in asexual microbes, and with inferences of divergence in the presence of gene-flow in natural sexual populations. This experiment shows that sex may be of benefit in heterogeneous environments, and thus helps explain why sex has been maintained more generally.     

Evolution of a single niche specialist in variable environments

The pattern (space versus time) and scale (relative to the lifetime of individuals) of environmental variation is thought to play a central role in governing the evolution of the ecological niche and the maintenance of genetic variance in fitness. To evaluate this idea, we serially propagated an initially genetically uniform population of the bacterium Pseudomonas fluorescens for a few hundred generations in environments that differed in both the pattern and scale at which two highly contrasted carbon substrates were experienced. We found that, contrary to expectations, populations often evolved into a single niche specialist adapted to the less-productive substrate in variable environments and that the genetic variance in fitness across different components of the environment was not generally higher in variable environments when compared with constant environments. We provide evidence to suggest that our results reflect a novel constraint on niche evolution imposed by the supply of beneficial mutations available to selection in variable environments.     

Diverse phenotypic and genetic responses to short‐term selection in evolving Escherichia coli populations

Beneficial mutations fuel adaptation by altering phenotypes that enhance the fit of organisms to their environment. However, the phenotypic effects of mutations often depend on ecological context, making the distribution of effects across multiple environments essential to understanding the true nature of beneficial mutations. Studies that address both the genetic basis and ecological consequences of adaptive mutations remain rare. Here, we characterize the direct and pleiotropic fitness effects of a collection of 21 first‐step beneficial mutants derived from naïve and adapted genotypes used in a long‐term experimental evolution of Escherichia coli. Whole‐genome sequencing was able to identify the majority of beneficial mutations. In contrast to previous studies, we find diverse fitness effects of mutations selected in a simple environment and few cases of genetic parallelism. The pleiotropic effects of these mutations were predominantly positive but some mutants were highly antagonistic in alternative environments. Further, the fitness effects of mutations derived from the adapted genotypes were dramatically reduced in nearly all environments. These findings suggest that many beneficial variants are accessible from a single point on the fitness landscape, and the fixation of alternative beneficial mutations may have dramatic consequences for niche breadth reduction via metabolic erosion.     

Selective Pressure Causes an RNA Virus to Trade Reproductive Fitness for Increased Structural and Thermal Stability of a Viral Enzyme

The modulation of fitness by single mutational substitutions during environmental change is the most fundamental consequence of natural selection. The antagonistic tradeoffs of pleiotropic mutations that can be selected under changing environments therefore lie at the foundation of evolutionary biology. However, the molecular basis of fitness tradeoffs is rarely determined in terms of how these pleiotropic mutations affect protein structure. Here we use an interdisciplinary approach to study how antagonistic pleiotropy and protein function dictate a fitness tradeoff. We challenged populations of an RNA virus, bacteriophage Φ6, to evolve in a novel temperature environment where heat shock imposed extreme virus mortality. A single amino acid substitution in the viral lysin protein P5 (V207F) favored improved stability, and hence survival of challenged viruses, despite a concomitant tradeoff that decreased viral reproduction. This mutation increased the thermostability of P5. Crystal structures of wild-type, mutant, and ligand-bound P5 reveal the molecular basis of this thermostabilization—the Phe207 side chain fills a hydrophobic cavity that is unoccupied in the wild-type—and identify P5 as a lytic transglycosylase. The mutation did not reduce the enzymatic activity of P5, suggesting that the reproduction tradeoff stems from other factors such as inefficient capsid assembly or disassembly. Our study demonstrates how combining experimental evolution, biochemistry, and structural biology can identify the mechanisms that drive the antagonistic pleiotropic phenotypes of an individual point mutation in the classic evolutionary tug-of-war between survival and reproduction.     

Pleiotropic effects of beneficial mutations in Escherichia coli

Micromutational models of adaptation have placed considerable weight on antagonistic pleiotropy as a mechanism that prevents mutations of large effect from achieving fixation. However, there are few empirical studies of the distribution of pleiotropic effects, and no studies that have examined this distribution for a large number of adaptive mutations. Here we examine the form and extent of pleiotropy associated with beneficial mutations in Escherichia coli. To do so, we used a collection of independently evolved genotypes, each of which contains a beneficial mutation that confers increased fitness in a glucose-limited environment. To determine the pleiotropic effects of these mutations, we examined the fitnesses of the mutants in five novel resource environments. Our results show that the majority of mutations had significant fitness effects in alternative resources, such that pleiotropy was common. The predominant form of this pleiotropy was positive--that is, most mutations that conferred increased fitness in glucose also conferred increased fitness in novel resources. We did detect some deleterious pleiotropic effects, but they were primarily limited to one of the five resources, and within this resource, to only a subset of mutants. Although pleiotropic effects were generally positive, fitness levels were lower and more variable on resources that differed most in their mechanisms of uptake and catabolism from that of glucose. Positive pleiotropic effects were strongly correlated in magnitude with their direct effects, but no such correlation was found among mutants with deleterious pleiotropic effects. Whereas previous studies of populations evolved on glucose for longer periods of time showed consistent declines on some of the resources used here, our results suggest that deleterious pleiotropic effects were limited to only a subset of the beneficial mutations available.     

Emergence of mammalian cell-adapted vesicular stomatitis virus from persistent infections of insect vector cells

Arboviruses (arthropod-borne viruses) represent quintessential generalists, with the ability to infect and perform well in multiple hosts. However, antagonistic pleiotropy imposed a cost during the adaptation to persistent replication of vesicular stomatitis virus in sand fly cells and resulted in strains that initially replicated poorly in hamster cells, even when the virus was allowed to replicate periodically in the latter. Once a debilitated strain started replicating continuously in mammalian cells, fitness increased significantly. Fitness recovery did not entail back mutations or compensatory mutations, but instead, we observed the replacement of persistence-adapted genomes by mammalian cell-adapted strains with a full set of new, unrelated sequence changes. These mammalian cell-adapted genomes were present at low frequencies in the populations with a history of persistence for up to a year and quickly became dominant during mammalian infection, but coexistence was not stable in the long term. Periodic acute replication in mammalian cells likely contributed to extending the survival of minority genomes, but these genomes were also found in strictly persistent populations.     

Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses

In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments.     

EVOLUTIONARY ADAPTATION TO TEMPERATURE II. THERMAL NICHES OF EXPERIMENTAL LINES OF ESCHERICHIA COLI

Groups of replicated lines of the bacterium Escherichia coli were propagated for 2,000 generations at constant 32, 37, or 42°C, or in an environment that alternated between 32 and 42°C. Here, we examine the performance of each group across a temperature range of 12-44°C measuring the temperatures over which each line can maintain itself in serial dilution culture (the thermal niche). Thermal niche was not affected by selection history: average lower and upper limits remained about 19 and 42°C for all groups. In addition, no significant differences among groups were observed in rate of extinction at more extreme temperatures. Within the thermal niche, we measured the mean fitness of the evolved groups relative to their common ancestor. Increases in mean fitness were temperature specific, with the largest increase for each group occurring near its selected temperature. Thus, the temperature at which mean fitness relative to the ancestor was greatest (the thermal optimum) diverged by about 10°C for the groups selected at constant 32°C versus constant 42°C. Tradeoffs in relative fitness (decrements relative to the ancestor elsewhere within the thermal niche) did not necessarily accompany fitness improvements, although tradeoffs were observed for a few of the lines. We conclude that adaptation in this system was quite temperature specific, but substantial divergence among groups in thermal optima had little effect on the limits of their thermal niches and did not necessarily involve tradeoffs in fitness at other temperatures.     

Evolutionary genetics of plant adaptation

Plants provide unique opportunities to study the mechanistic basis and evolutionary processes of adaptation to diverse environmental conditions. Complementary laboratory and field experiments are important for testing hypotheses reflecting long-term ecological and evolutionary history. For example, these approaches can infer whether local adaptation results from genetic tradeoffs (antagonistic pleiotropy), where native alleles are best adapted to local conditions, or if local adaptation is caused by conditional neutrality at many loci, where alleles show fitness differences in one environment, but not in a contrasting environment. Ecological genetics in natural populations of perennial or outcrossing plants can also differ substantially from model systems. In this review of the evolutionary genetics of plant adaptation, we emphasize the importance of field studies for understanding the evolutionary dynamics of model and nonmodel systems, highlight a key life history trait (flowering time) and discuss emerging conservation issues.     

Pleiotropic costs of niche expansion in the RNA bacteriophage phi 6

Natural and experimental systems have failed to universally demonstrate a trade-off between generalism and specialism. When a trade-off does occur it is difficult to attribute its cause to antagonistic pleiotropy without dissecting the genetic basis of adaptation, and few previous experiments provide these genetic data. Here we investigate the evolution of expanded host range (generalism) in the RNA virus phi6, an experimental model system allowing adaptive mutations to be readily identified. We isolated 10 spontaneous host range mutants on each of three novel Pseudomonas hosts and determined whether these mutations imposed fitness costs on the standard laboratory host. Sequencing revealed that each mutant had one of nine nonsynonymous mutations in the phi6 gene P3, important in host attachment. Seven of these nine mutations were costly on the original host, confirming the existence of antagonistic pleiotropy. In addition to this genetically imposed cost, we identified an epigenetic cost of generalism that occurs when phage transition between host types. Our results confirm the existence in phi6 of two costs of generalism, genetic and environmental, but they also indicate that the cost is not always large. The possibility for cost-free niche expansion implies that varied ecological conditions may favor host shifts in RNA viruses.     

Vesicular stomatitis virus evolution during alternation between persistent infection in insect cells and acute infection in mammalian cells is dominated by the persistence phase

Vesicular stomatitis virus has the potential for very rapid evolution in the laboratory, but like many other arboviruses, it evolves at a relatively slow rate in the natural environment. Previous work showed that alternating replication in different cell types does not promote stasis. In order to determine whether other factors promote stasis, we compared the fitness trajectories of populations evolving during acute infections in mammalian cells, populations evolving during persistent infections in insect cells, and populations evolving during alternating acute and persistent infection cycles. Populations evolving under constant conditions increased in fitness in the environment in which they replicated. An asymmetric trade-off was observed such that acute infection had no cost for persistence but persistent replication had a dramatic cost for acute infection in mammalian cells. After an initial period of increase, fitness remained approximately constant in all the populations that included persistent replication, but fitness continuously increased in populations evolving during acute infections. Determination of the consensus sequence of the genes encoding the N, P, M, and G proteins showed that the pattern of mutation accumulation was coherent with fitness changes during persistence so that once fitness reached a maximum, the rate of mutation accumulation dropped. Persistent replication dominated both the genetic and the phenotypic evolution of the populations that alternated between acute infection of mammalian cells and persistence in insect cells, and fitness loss was observed in the mammalian environment despite periodic replication in mammalian cells. These results show that stasis can be achieved without good levels of adaptation to both the mammalian and the insect environments.     

The basis of antagonistic pleiotropy in hfq mutations that have opposite effects on fitness at slow and fast growth rates

Mutations beneficial in one environment may cause costs in different environments, resulting in antagonistic pleiotropy. Here, we describe a novel form of antagonistic pleiotropy that operates even within the same environment, where benefits and deleterious effects exhibit themselves at different growth rates. The fitness of hfq mutations in Escherichia coli affecting the RNA chaperone involved in small-RNA regulation is remarkably sensitive to growth rate. E. coli populations evolving in chemostats under nutrient limitation acquired beneficial mutations in hfq during slow growth (0.1 h⁻¹) but not in populations growing sixfold faster. Four identified hfq alleles from parallel populations were beneficial at 0.1 h⁻¹ and deleterious at 0.6 h⁻¹. The hfq mutations were beneficial, deleterious or neutral at an intermediate growth rate (0.5 h⁻¹) and one changed from beneficial to deleterious within a 36 min difference in doubling time. The benefit of hfq mutations was due to the greater transport of limiting nutrient, which diminished at higher growth rates. The deleterious effects of hfq mutations at 0.6 h⁻¹ were less clear, with decreased viability a contributing factor. The results demonstrate distinct pleiotropy characteristics in the alleles of the same gene, probably because the altered residues in Hfq affected the regulation of expression of different genes in distinct ways. In addition, these results point to a source of variation in experimental measurement of the selective advantage of a mutation; estimates of fitness need to consider variation in growth rate impacting on the magnitude of the benefit of mutations and on their fitness distributions.     

Origin, fate, and architecture of ecologically relevant genetic variation

Recent advances in molecular genetics combined with field manipulations are yielding new insight into the origin, evolutionary fate, and genetic architecture of phenotypic variation in natural plant populations, with two surprising implications for the evolution of plant genomes. First, genetic loci exhibiting antagonistic pleiotropy across natural environments appear rare relative to loci that are adaptive in one or more environments and neutral elsewhere. These 'conditionally neutral' alleles should sweep to fixation when they arise, yet genome comparisons find little evidence for such selective sweeps. Second, genes under biotic selection tend to be of larger effect than genes under abiotic selection. Recent theory suggests this may be a consequence of high gene flow among populations under selection for local adaptation.     

THE EFFECT OF NICHE PREFERENCE ON POLYMORPHISM PROTECTION IN A HETEROGENEOUS ENVIRONMENT

A model is proposed in which niche choice precedes natural selection in an individual's life span; the panmictic population occupies an environment divided into niches, each contributing a constant proportion of parents to the next generation. Niche choice and fitness within the niche are controlled either by the same locus or by two linked loci. The conditions for a protected polymorphism are derived. It is shown that niche preferences can increase the protective effect of natural selection over a polymorphism. This effect depends on the existence of a positive correlation between preference for a niche and relative fitness within that niche, and also on the relative size of the niches. In the absence of within-niche fitness differences, alleles that cause preference for different niches can still be protected. Alleles that determine preference for niches contributing little to the total population can be eliminated by the ability to choose between niches.     

Experimental evolution for generalists and specialists reveals multivariate genetic constraints on thermal reaction norms

Theory predicts the emergence of generalists in variable environments and antagonistic pleiotropy to favour specialists in constant environments, but empirical data seldom support such generalist–specialist trade‐offs. We selected for generalists and specialists in the dung fly Sepsis punctum (Diptera: Sepsidae) under conditions that we predicted would reveal antagonistic pleiotropy and multivariate trade‐offs underlying thermal reaction norms for juvenile development. We performed replicated laboratory evolution using four treatments: adaptation at a hot (31 °C) or a cold (15 °C) temperature, or under regimes fluctuating between these temperatures, either within or between generations. After 20 generations, we assessed parental effects and genetic responses of thermal reaction norms for three correlated life‐history traits: size at maturity, juvenile growth rate and juvenile survival. We find evidence for antagonistic pleiotropy for performance at hot and cold temperatures, and a temperature‐mediated trade‐off between juvenile survival and size at maturity, suggesting that trade‐offs associated with environmental tolerance can arise via intensified evolutionary compromises between genetically correlated traits. However, despite this antagonistic pleiotropy, we found no support for the evolution of increased thermal tolerance breadth at the expense of reduced maximal performance, suggesting low genetic variance in the generalist–specialist dimension.     

The Origins of Specialization: Insights from Bacteria Held 25 Years in Captivity

Examples of ecological specialization abound in nature but the evolutionary and genetic causes of tradeoffs across environments are typically unknown. Natural selection itself may favor traits that improve fitness in one environment but reduce fitness elsewhere. Furthermore, an absence of selection on unused traits renders them susceptible to mutational erosion by genetic drift. Experimental evolution of microbial populations allows these potentially concurrent dynamics to be evaluated directly, rather than by historical inference. The 50,000 generation (and counting) Lenski Long-Term Evolution Experiment (LTEE), in which replicate E. coli populations have been passaged in a simple environment with only glucose for carbon and energy, has inspired multiple studies of their potential specialization. Earlier in this experiment, most changes were the side effects of selection, both broadening growth potential in some conditions and narrowing it in others, particularly in assays of diet breadth and thermotolerance. The fact that replicate populations experienced similar losses suggested they were becoming specialists because of tradeoffs imposed by selection. However a new study in this issue of PLOS Biology by Nicholas Leiby and Christopher Marx revisits these lines with powerful new growth assays and finds a surprising number of functional gains as well as losses, the latter of which were enriched in populations that had evolved higher mutation rates. Thus, these populations are steadily becoming glucose specialists by the relentless pressure of mutation accumulation, which has taken 25 years to detect. More surprising, the unpredictability of functional changes suggests that we still have much to learn about how the best-studied bacterium adapts to grow on the best-studied sugar.The wonder of biological diversity belies a puzzling subtext. Species are defined as much by their limits as their capabilities. Very few species in our common vernacular tolerate life in a wide range of environments, and those that do—the Norway rat, say—are not generally appealing. More often, we celebrate specialization to a particular condition: for example, orchid epiphytes growing tenuously in the cloud forest, only a subtle climate shift from extinction. Even grade school natural history teaches us that species are often unfit when living beyond their natural range.So it comes as a surprise that the causes of this rampant ecological specialization are poorly understood. “Use it or lose it,” but why? One common explanation is that natural selection tends to favor traits that simultaneously enhance fitness in one environment but compromise fitness elsewhere. This selective process is known as “antagonistic pleiotropy.” Another explanation is that a selective shadow falls upon unused traits, rendering them susceptible to mutational erosion by random genetic drift. This neutral process is known as “mutation accumulation” (Figure 1). These processes inevitably co-occur, and can be enhanced by the hybrid dynamic of genetic hitchhiking, in which neutral mutations affecting unused functions become linked to different mutations under positive selection. In most cases, the functional decay of a species can only be studied retrospectively, and distinguishing the roles of antagonistic pleiotropy and mutation accumulation is hampered by weak historical inference. Did selection, or an absence of selection, produce the blind cavefish [1]? There is little controversy that the sum of these dynamics can produce specialists, but their timing and relative importance is an open question.Open in a separate windowFigure 1Hypothetical dynamics of fitness in foreign environments by pleiotropy or mutation accumulation during long-term adaptation.Prolonged adaptation to one environment leads to decelerating fitness gains in the selective environment (solid black line), as beneficial mutations become limiting. Consequences of this adaptation for fitness in other environments may take different forms. No net change may occur if beneficial mutations generate no or inconsistent side effects (neutrality). However, the same mutations responsible for adaptation may also increase fitness in other environments (synergistic pleiotropy, dotted line), may decrease fitness in foreign environments at an equivalent rate if antagonistic effects correlate with selected effects (antagonistic pleiotropy, dotted line), or may decrease fitness at an increasing rate if subsequent mutations generate greater tradeoffs (antagonistic pleiotropy, dashed and dotted line). The uncertainty of the form of pleiotropic effects reflects a general lack of understanding of how mutations interact to affect fitness, particularly over the long term. Mutation accumulation (MA) in traits hidden from selection is expected to reduce fitness randomly but linearly on average, more slowly during evolution at a low mutation rate (MA, low U) or more rapidly at a high mutation rate (MA, high U). Evidence of all processes is now evident in this latest study of the evolution of diet breadth in the LTEE [20].The study of “evolution in action” using model experimental populations of rapidly reproducing organisms allows researchers to quantify both adaptation and any functional declines simultaneously. This approach is especially powerful when samples of evolving populations can be stored inanimate and studied at a later time under various conditions. Perhaps the best example of this approach is Richard Lenski''s Long-Term Evolution Experiment (LTEE), in which 12 populations of E. coli have been grown under simple conditions for more than 25 years and 50,000 generations [2],[3].When as a graduate student I wondered aloud whether the LTEE lines had become specialists, a colleague remarked: “Of course! You''ve selected for streamlined E. coli that have scuttled unused functions.” But with only a small amount of glucose as the sole carbon source available to the ancestor (the innovation by one population of using citrate for growth more than 30,000 generations in the future notwithstanding [4]), all anabolic pathways to construct new cells remain under strong selection to preserve their function. Moreover, because some catabolic reactions use the same intermediates as anabolic pathways (a form of pleiotropy) [5], growth on alternative carbon sources may be nonetheless preserved. Thus, we wondered whether the physiology of E. coli might actually prove to be robust during long-term evolution on glucose alone.Over the first 2,000 generations, the LTEE lines gained more often than lost fitness across a range of different environments [6]. In addition, a high-throughput screen of cellular respiration (Biolog) for the best-studied clone from these lines showed 171 relative gains and only 32 losses [7]. Even these losses in substrate respiration did not translate to reduced fitness versus the ancestor; rather, the evolved clone was simply relatively worse in the foreign resources than in glucose [7]. Evidently, each of the five beneficial mutations found in this early clone was broadly beneficial and imparted few tradeoffs [8]. Generalists rather than specialists were the rule.Between 2,000 and 20,000 generations, fitness losses in foreign conditions became more obvious but not always consistent. Some lines became less fit than the ancestor in a dilute complex medium (LB) [9], all lines grew worse at high (>40°C) and low (<20°C) temperature [10], and all lines became sensitive to the resource concentration in their environment, even for glucose [9]. Did subsequent beneficial mutations cause these tradeoffs (antagonistic pleiotropy), or did other, neutral or slightly harmful mutations accumulate by drift (Figure 1)? We must consider the population genetic dynamics of these LTEE populations. The hallmark of neutral theory [11] is that mutations with no effect in the selective environment should become fixed in the population at the rate of mutation. For the ancestor of this experiment, the mutation rate is ∼10⁻³ per genome per generation [12],[13], so only a handful of neutral mutations would have fixed by the time tradeoffs became evident, and would not likely explain the early specialization.However, an important extension of neutral theory is that slightly harmful mutations—those whose effects are roughly the inverse of the population size or below, 1/N—can also be fixed by drift [14]. Millions of slightly deleterious mutations were produced in these populations, which cycled between 5×10⁶ and 5×10⁸ cells each day. Might these mutations account for tradeoffs over the first 10–20,000 generations? In small populations, the effect of these mutations can be substantial, which explains why bottlenecked populations may experience fitness declines or even the genome erosion frequently seen in bacterial endosymbionts [15]. But in the large LTEE populations, most deleterious mutations are weeded out by selection and only those with the slightest effects may accumulate over very long time scales. Thus, because these early losses tended to occur when adaptation in the selective environment was most rapid, and because the randomness and rarity of mutation accumulation should not produce parallel changes over these time scales, early specialization is best explained by antagonistic pleiotropy [9],[10].Later in the LTEE, elevated mutation rates began to evolve in certain lines, resulting in a fundamental change in the population genetic environment [16],[17] that should increase the rate of functional decay in unused, essentially neutral functions. These mutator populations tended to perform worse in multiple environments, and in theory should continue to specialize more rapidly by accelerated mutation accumulation. As a first test, we used Biolog plates to assay respiration on 95 different carbon sources over the first 20,000 generations [18]. Although mutators tended to exhibit a reduced breadth of function in this assay, the difference was not statistically significant [18]. Rather, a surprising number of losses of function were shared among replicate lines, and we took this parallelism as further support of antagonistic pleiotropy driven by selection for common sets of adaptive mutations.Here the LTEE offers its greatest advantage: more time, both for evolution and innovative research. Over subsequent generations, mutator lines should continue to accumulate greater mutational load by drift and hence become more specialized than lines retaining the low ancestral rate. Genomic sequences of the evolved lines now have confirmed this increased mutational load [3],[19] in the six of 12 lines that are now mutators [16]. In this issue, Leiby and Marx [20] have readdressed these questions by retracing old steps, applying the prior Biolog assays to lines spanning 50,000 generations of evolution, and by pioneering new high-throughput assays of fitness in many resources. Somewhat surprisingly, these methods disagree and challenge the reliability of Biolog data as a fitness proxy. As a proprietary measure of cellular respiration, it can demonstrate major functional shifts but is less reliable than growth rate as a fitness parameter.More importantly, Leiby and Marx provide clear evidence that niche breadth in the LTEE was shaped by both mutation accumulation and pleiotropy. Growth rates actually increased on several resources, and hence the pleiotropic effects of adaptation to glucose were synergistic, broadening functionality particularly over the first 20,000 generations, as well as antagonistic, producing fewer tradeoffs than previously thought [20]. Pleiotropic effects were also somewhat unpredictable: a sophisticated flux-balance analysis [21] of foreign substrates did not reveal more gains for resources similar to glucose or losses for dissimilar resources. Some early losses linked to selection (maltose, galactose, serine) [6] became complete, but also subtle gains of function for dicarboxylic acid metabolism, perhaps related to growth on metabolic byproducts, became amplified. The most striking pattern was that mutator populations became specialists, diminished for many functions owing to their greater mutational burden, and this only became evident after 50,000 generations in a single resource. These convergent functional losses were not caused by selection, as is often argued, but rather by an absence of selection in the face of mutational pressure. Mutational decay by genetic drift takes a long time, and it will take much longer for the non-mutator lines, it seems.Although Leiby and Marx [20] correctly emphasize the importance of truly long-term selection combined with deficient DNA repair to reveal effects of mutation accumulation, decay has been witnessed in other systems undergoing regular population bottlenecks over shorter time scales [22],[23]. Antagonistic pleiotropy can also reveal its effects much more rapidly than was seen in the LTEE, especially when selection discriminates among discrete fitness features in a heterogeneous environment, such as in the colonization of a new landscape [24],[25]. What this study uniquely illustrates is the unpredictability of pleiotropic effects of adaptation to a simple environment, which in turn shows how chance draws from a distribution of contending beneficial mutations may produce divergent outcomes, ranging from generalists to specialists. A sample of the first mutants competing to prevail in the LTEE system showed variable niche breadth [26] so perhaps we should not be surprised that the footprints of these large-effect mutations endure. Further study of the precise mechanisms by which different mutations produce more fit offspring will teach us more about the origins of diversity that beguile us. We can also gain a broader perspective on the longstanding tension between chance and necessity [27]—a motivator of the LTEE—by focusing more on what is unnecessary, such as how organisms grow in foreign environments. Often insight comes from studying at the margins of a problem, and here, the limits to the growth of these bacteria have allowed us to focus more on how exactly they have accomplished their most essential tasks.     

Experimental adaptive radiation in Pseudomonas

We studied the importance of selection and constraint in determining the limits of adaptive radiation and the consequences of adaptive radiation in an experimental system. We propagated four replicate lines of the bacterium Pseudomonas fluorescens derived from a single ancestral clone in 95 environments, where growth was limited by the availability of a single carbon source for 1,000 generations. We then assayed the growth of the ancestral clone and the evolved lines in all 95 environments. Evolved lines increased their performance in almost every selection environment and invaded 70% of the novel environments as a direct response to selection. Direct responses tended to be larger in environments where growth was initially poor. Although evolved lines lost the ability to grow on about three substrates that their ancestor could readily grow on, the correlated response to selection was, on average, positive. The correlated response allowed all of our evolved populations to expand their niches and to occupy collectively the remaining novel habitats. This is inconsistent with classical theories of niche evolution. In the most extreme cases, adaptation occurred through "roundabout selection": lineages became adapted to an environment through selection in another environment but not through selection in the environment itself. Our results indicate that mutation accumulation by neutral drift was responsible for generating the majority of costs of adaptation.