Chapter

Phenotypic and Genomic Evolution during a 20,000‐Generation Experiment with the Bacterium Escherichia coli

Authors:
To read the full-text of this research, you can request a copy directly from the author.

Abstract

Introduction Phenotypic and Genomic Evolution Conclusions Literature Cited

No full-text available

Request Full-text Paper PDF

To read the full-text of this research,
you can request a copy directly from the author.

... En este caso los organismos mutantes tienen una ventaja y el gen mutado eventualmente reemplaza al original por selección natural. Estas mutaciones se fijan y pueden ser observadas en la gran mayoría de la descendencia [1, 2, 3], constituyen una nueva característica del genotipo de la especie. La influencia del ambiente es esencial en el proceso selectivo porque es quien dicta las reglas de la competencia, determina significativamente las características fenotípicas de los organismos y también, de manera indirecta a través de las mutaciones, las características genotípicas promedio de la población. ...
... En varias poblaciones del EELP aparece un " mutante " , es decir, un genotipo donde la frecuencia de mutaciones aumenta aproximadamente 100 veces respecto a la cepa ancestral [2]. En la Fig (2.10),tomada de la Ref [2], se muestra la frecuencia de mutaciones ante un antibiótico de las diferentes poblaciones del EELP, cuando se alcanza un número de generaciones N gen = 10000. ...
... En varias poblaciones del EELP aparece un " mutante " , es decir, un genotipo donde la frecuencia de mutaciones aumenta aproximadamente 100 veces respecto a la cepa ancestral [2]. En la Fig (2.10),tomada de la Ref [2], se muestra la frecuencia de mutaciones ante un antibiótico de las diferentes poblaciones del EELP, cuando se alcanza un número de generaciones N gen = 10000. Se observan 3 poblaciones donde el mutante se ha impuesto como genotipo dominante. ...
Article
Full-text available
This thesis is aimed at studying mutations, understood as trajectories in the DNA configuration space. An evolutive model of mutations in terms of Levy flights is proposed. The parameters of the model are estimated by means of data from the Long-Term Evolution Experiment (LTEE) with {\it E. Coli} bacteria. The results of simulations on competition of clones, mean fitness, etc are compared with experimental data. We discuss the qualitative analogy found between the bacterial mutator phenotype and the cancerous cells. The role of radiation as source of mutations is analyzed. We focus on the case of Radon's decay in the lungs in breathing.
... Cells exposed to the shower of electrons and ions, caused by the collision of a neutron and a proton of water, could be anihilated or experience a permanent damage, in particular, a damage in the DNA. The frequency of such events is similar to the rate of appearance of mutations with damage in the DNA repair mechanism [4], as measured in the Long Term Evolution Experiment (LTEE), where E. Coli populations evolve under controlled conditions [5]. ...
... The dependence 2 t/t0 is due to the way of reproduction, by cellular division. The experiment shows a set of very interesting results [4]. We shall stress only two of them. ...
... The fact that mutations with damage in the DNA repair mechanism are deleterious [4] is also consistent with the nature of BNR ionization processes. Indeed, the electron and ion shower is highly energetic and may produce such damages in the DNA, especially in the first steps after the n+p collision. ...
Article
Full-text available
We suggest a possible correlation between the ionization events caused by the background neutron radiation and the experimental data on mutations with damage in the DNA repair mechanism, coming from the Long Term Evolution Experiment in E. Coli populations.
... �e term teleology in the context of 'teleological explanations' can also refer to dualistic explanations. �is type of explanation, which is based on the Platonic model, sees the world as the end-product of a divine cra�sman [Lennox 1992]. �is is sometimes described by the term 'external' or 'extrinsic' teleology. ...
... �e notion of " immanence " may simply stress that the goal or function involved is a goal or function of the individual organism under consideration, rather than of an " external " designer. But it may also carry connotations of " quasi-conscious " agent inside natural objects, so to speak […]' [Lennox 1992]. �is term is associated with the philosophy of Aristotle, but despite the fact that there is unanimity on the importance of teleology to Aristotle, there is no consensus about which meaning Aristotle adhered to [ Johnson 2005]. ...
... On se xua l r eproduct ion contribute (or are directed) to some end, they take place and exist because they contribute to an end [Lennox 1992] . Whereas naturalism and theism only assume the existence of efficient causes, �nalism explains processes and function additionally by reference to �nal causes. ...
... The E. coli LTEE is described in detail elsewhere [11,12] . Our analyses used whole-population samples from nine of the 12 LTEE populations taken at three time points: 40 000, 50 000 and 60 000 generations (electronic supplementary material, table S1), for a total of 27 samples. ...
... The culture conditions for the LTEE are described elsewhere [11,12]. In brief, each population is maintained by transferring 0.1 ml of culture into 9.9 ml of fresh medium every 24 h. ...
... One source of among-population variability is that three of the nine populations in our study had evolved hypermutability, such that their point-mutation rates increased by roughly 100-fold [8,13]. Both theory and prior empirical evidence indicate that these hypermutable populations should increase in fitness somewhat faster than populations with the ancestral mutation rate, at least so long as there remain some point mutations that confer fitness benefits substantially above the increased load of deleterious mutations suffered by the hypermutators [4,12,13,24]. Indeed, we see that all three hypermutator populations-Araþ3, Ara-1 and Ara-4have higher mean fitness than any of the other six populations at all three time points tested here (electronic supplementary material, table S2). ...
Article
Full-text available
Many populations live in environments subject to frequent biotic and abiotic changes. Nonetheless, it is interesting to ask whether an evolving population's mean fitness can increase indefinitely, and potentially without any limit, even in a constant environment. A recent study showed that fitness trajectories of Escherichia coli populations over 50 000 generations were better described by a power-law model than by a hyperbolic model. According to the power-law model, the rate of fitness gain declines over time but fitness has no upper limit, whereas the hyperbolic model implies a hard limit. Here, we examine whether the previously estimated power-law model predicts the fitness trajectory for an additional 10 000 generations. To that end, we conducted more than 1100 new competitive fitness assays. Consistent with the previous study, the power-law model fits the new data better than the hyperbolic model. We also analysed the variability in fitness among populations, finding subtle, but significant, heterogeneity in mean fitness. Some, but not all, of this variation reflects differences in mutation rate that evolved over time. Taken together, our results imply that both adaptation and divergence can continue indefinitely—or at least for a long time—even in a constant environment.
... By substituting the organism with its genes, and assigning to each allele a fitness value, population genetics models can thus explain how and why some traits increase their frequencies in a population while others tend to disappear: evolution is explained by postulating that it corresponds to changes in alleles' frequencies. Under such simplifications and assumptions, it is not surprising that the population genetics models work best for simple organisms like the asexually reproducing bacteria E. coli, as in Lenski's long-term evolution experiment (Lenski 2003, Dawkins 2009). Starting from 12 identical populations in 15 The idea that characters' transmission is Boolean rescues Darwinism from the problem of how to avoid homogeneity in a population after a few generations. ...
... (In Wikipedia, The Free Encyclopedia. Retrieved 09:26, September 13, 2019, from https://en.wikipedia.org/w/index.php?title=Variance&oldid=911844733) 23 The concept of 'magnitude of effect' of a mutation is open to interpretation: if acquiring a new metabolic capacity is considered a 'large effect', Lenski's experiments (Lenski 2003) would invalidate Fisher's statement (thanks to Davide Vecchi for this comment). 24 Genes' effects are additive if each gene contributes to the phenotype independently. ...
... […] (Stebbins 1966: 12) But: is it so? The modern synthesis transformed evolutionary biology into a formal science, able to explain and forecast the fate of populations through falsifiable hypotheses and repeatable experiments, such as Lenski's famous E. coli long-term evolution investigation (Lenski & Janick 2003). that appear everywhere in the natural world? ...
Thesis
Full-text available
Darwin aimed, with his theory of descent with modification through natural selection, to account for three biological explananda: the variety of living forms; the complexity of organisms, apparently increasing through the history of life; and adaptedness, or the fit of organisms to their environment. The success of this original research project 150 years after the publication of the Origin is uneven. The Modern Synthesis, unifying Darwinism and genetics, formalizes, through population genetics, the first claim: traits in a population spread, get fixed, are lost and slowly change into new ones according to their fitness and to the strength of selection. On the other hand, population genetics does not make any claim about complexity, let alone about its putative increase. Darwin’s theory is also the only known explanans for adaptedness. The evolutionary mindset known as adaptationism studies species’ traits and provides explanations about their adaptive origin. A mayor limitation of adaptationist explanations is their narrative nature: they cannot be tested. Several models have been proposed to overcome this limitation, from optimization programs to the ambitious Formal Darwinism Project by Alan Grafen. These proposals, however, focus on traits separately, and ignore the complexities of the architecture of organisms. The issue of complexity thus remains either unaddressed (by population genetics) or taken for granted (by adaptationism): the modern synthesis simply claims that complex traits appears from mutations and recombination shaped slowly and incrementally by selection. Complexity comes from a Deus-ex-Machina hidden in the environment. This approach, more and more challenged in the last decades, ignores many phenomena that do seem to affect phenotypic evolution, and that are accounted for by alternative, non-purely selective accounts. Many of them have been collected under the name of Extended Evolutionary Synthesis (Laland et al. 2015). The range of phenomena targeted by these accounts spans from chemical-physical laws, to genetic (e.g. Cherniak & Rodriguez-Esteban 2013, Kimura 1983, Wagner 2015), developmental (e.g. Maynard Smith et al. 1985), systemic (e.g. Kauffman 2000) and neo-Lamarckian mechanisms (e.g. Koonin & Wolf 2009). None of these accounts denies the importance and even preponderance of selection in the history of life, and they rather aim at integrating non-selective phenomena into Neo-Darwinism (a view known as ‘pluralism’). Although criticized by main-stream biology, we believe that pluralistic views and classical Neo-Darwinism can be integrated into a unified vision of evolution that formally accounts for organismal complexity. In the first place, we propose a definition of organismal architecture as form and function, going beyond the adaptationist consideration of organisms as just the sum of their optimised traits. In the second place, we suggest that fitness, being an intrinsically selective measure, should not be used to judge non-selective phenomena. We propose to use robustness instead, and we show how some non-selective forces impact the robustness of phenotypes. Finally, we present a model of evolutionary changes that maps populations as areas in a bi-dimensional space of fitness and robustness, where the effect of selection and of non-selective forces on shape and position of these areas can be tracked. Complexity, interpreted as organismal architecture, thus appears to be the result of several synchronic processes, among which selection plays an important but not always a preponderant role.
... The longest-running and best studied PRE is Richard Lenski's E. coli Long-Term Evolution Experiment (LTEE). The LTEE began on February 24, 1988 with the founding of twelve populations from a single clone of E. coli B (Lenski et al. 1991; Lenski 2004). Save for a neutral genetic marker that allows six populations to grow on arabinose (Ara + ), all were initially identical. ...
... Each day, 1% of each population is transferred to fresh medium, after which each grows 100-fold, or ~6.7 generations (Lenski et al. 1991). This serial transfer regime produces a " seasonality " in which a short feast of abundant glucose after transfer is followed by famine until the next transfer (Vasi, Travisano, and Lenski 1994; Lenski 2004). Each population has evolved for more than 60,000 generations since the experiment began, and population samples have been frozen every 500 generations throughout, providing an extensive fossil record that represents a rich resource for research (Lenski 2004). ...
... This serial transfer regime produces a " seasonality " in which a short feast of abundant glucose after transfer is followed by famine until the next transfer (Vasi, Travisano, and Lenski 1994; Lenski 2004). Each population has evolved for more than 60,000 generations since the experiment began, and population samples have been frozen every 500 generations throughout, providing an extensive fossil record that represents a rich resource for research (Lenski 2004). Remarkable evolutionary parallelism has been observed in the LTEE. ...
... How do the results obtained in this chapter bear on the interpretation of those experiments? Comparison to experiments where N e < 1/v: The most extensive laboratory evolution experiment to date has been performed under the direction of Richard Lenski at Michigan State University[18]. Starting in the early 1990s, Lenski and colleagues began growing 10 ml cultures of E. coli, which undergo six to seven doublings per day. Each day they transferred 1% of the culture to fresh medium. ...
... The rate of nucleotide mutations per generation of E. coli is ∼5 × 10 −10[21]. The effective population size N e of Lenski's[18]cultures of E. coli is ∼2 × 10 7 , which is the harmonic mean between the initial population of the day's culture (5×10 6 ) and the final population of the day (5×10 8 ) if the population is assumed to double in discrete generations[11]. Substituting these numbers into equation 2 shows that r D/fx would be 1.47 — greater than one — if r s were one and r v were 100. ...
Conference Paper
Full-text available
Over the course of evolution organisms have adapted to their environments by mutating to gain new functions or to lose pre-existing ones. Because adaptation can occur by either of these modes, it is of basic interest to assess under what, if any, evolutionary circumstances one of them may predominate. Since mutation occurs at the molecular level, one must look there to discern if an adaptation involves gain- or loss-of-function. Here I present a simple, deterministic model for the occurrence and spread of adaptive gain-of-function versus loss-of-function mutations, and compare the results to laboratory evolution experiments and studies of evolution in nature. The results demonstrate that loss-of-function mutations generally have an intrinsic evolutionary rate advantage over gain-of-function mutations, but that the advantage depends radically on population size, ratio of selection coefficients of competing adaptive mutations, and ratio of the mutation rates to the adaptive states.
... À mesure que le génotype s'éloigne de l'optimum, la proportion des mutations avantageuses augmente et la distribution de s suit alors approximativement une loi Gamma dite déplacée (courbe orange dans l'Encadré 3). Par ailleurs, d'autres caractères phénotypiques présentent une évolution parallèle dans la majorité des 12 populations : accroissement du taux de croissance, diminution de la phase de latence, accroissement de la taille cellulaire, diminution des capacités cataboliques, modifications globales de l'expression des gènes, accroissement de la superhélicité négative de l'ADN (c'est-à-dire le degré d'enroulement du chromosome qui provoque l'activation de la transcription de gènes, donnée chez les bactéries comme permettant notamment une expression optimale des opérons d'ARN ribosomiques) (pour revues, Lenski 2004, Philippe et al. 2007). Le degré de parallélisme observé entre réplicats suggère que ces changements puissent être directement impliqués dans le processus à la base de l'adaptation. ...
... Cependant, même dans des environnements homogènes lors d'expériences d'évolution, des bactéries peuvent évoluer vers une différenciation écologique (Rosenzweig et al. 1994, Rozen et al. 2005), ce qui contraste avec les attendus de modèles simples qui prédisent le maintien de populations monomorphes au sein desquelles la sélection périodique de mutants de plus en plus adaptés (balayage sélectif) purge régulièrement la diversité génétique. Lors de la plus longue expérience d'évolution en cours conduite par Lenski (2004) sur E. coli, il a même été détecté ce qui peut être considéré comme la première étape d'un événement de spéciation (Rozen et al. 2005 ). En effet, deux écotypes bactériens phénotypiquement différenciés ont émergé à partir d'un ancêtre commun et coexistent depuis plusieurs dizaines de milliers de générations (Rozen et Lenski 2000). ...
... They have been employed in research to study basic life processes such as DNA transcription, translation and replication (Crick, Barnett, Brenner, & Tobin, 1961; Nirenberg et al., 1965; Judson, 1996). In the industry, they have been used in genetic engineering and pharmaceutical productions (Cohen, Chang, Boyer, & Helling, 1973; Huang, Lin, & Yang, 2012; Kawecki et al., 2013; Lenski, 2004; Schaechter & Neidhardt, 1987). Escherichia coli is a Gram negative bacilli which may possess whip-like flagella for locomotion or hair-like pili for attachment (Blount, 2015). ...
Thesis
A project work submitted to the Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana in partial fulfillment for the award of a BSc degree in Medical Laboratory Science.
... They have been employed in research to study basic life processes such as DNA transcription, translation and replication (Crick, Barnett, Brenner, & Tobin, 1961; Nirenberg et al., 1965; Judson, 1996). In the industry, they have been used in genetic engineering and pharmaceutical productions (Cohen, Chang, Boyer, & Helling, 1973; Huang, Lin, & Yang, 2012; Kawecki et al., 2013; Lenski, 2004; Schaechter & Neidhardt, 1987). Escherichia coli is a Gram negative bacilli which may possess whip-like flagella for locomotion or hair-like pili for attachment (Blount, 2015). ...
Thesis
A project work submitted to the Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana in partial fulfillment for the award of a BSc degree in Medical Laboratory Science.
... They have been employed in research to study basic life processes such as DNA transcription, translation and replication (Crick, Barnett, Brenner, & Tobin, 1961; Nirenberg et al., 1965; Judson, 1996). In the industry, they have been used in genetic engineering and pharmaceutical productions (Cohen, Chang, Boyer, & Helling, 1973; Huang, Lin, & Yang, 2012; Kawecki et al., 2013; Lenski, 2004; Schaechter & Neidhardt, 1987). Escherichia coli is a Gram negative bacilli which may possess whip-like flagella for locomotion or hair-like pili for attachment (Blount, 2015). ...
Thesis
A project work submitted to the Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana in partial fulfillment for the award of a BSc degree in Medical Laboratory Science.
... Such claims must one day be testable via our search for extraterrestrial intelligence (SETI), and by advances in science and simulation. Empirically, we can also look for universal developmental outcomes of experiments in rapid evolutionary systems, such as Richard Lenski's studies of E. coli mutation (Lenski 2004). Evolutionary convergences (developmental optima) should be increasingly demonstrable in multigenerational experiments in such systems, whenever their attractor states can be formally or even informally predicted using our advancing theories of physical chemistry, supramolecular chemistry, molecular biology, or genetics. ...
... They have been employed in research to study basic life processes such as DNA transcription, translation and replication (Crick, Barnett, Brenner, & Watts-Tobin, 1961;Nirenberg et al., 1965;Judson, 1996). In the industry, they have been used in genetic engineering and pharmaceutical productions (Cohen, Chang, Boyer, & Helling, 1973;Huang, Lin, & Yang, 2012;Kawecki et al., 2013;Lenski, 2004;Schaechter & Neidhardt, 1987). Escherichia coli is a Gram negative bacilli which may possess whip-like flagella for locomotion or hair-like pili for attachment (Blount, 2015). ...
Thesis
A project work submitted to the Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana in partial fulfillment for the award of a BSc degree in Medical Laboratory Science.
... They have been employed in research to study basic life processes such as DNA transcription, translation and replication (Crick, Barnett, Brenner, & Tobin, 1961; Nirenberg et al., 1965; Judson, 1996). In the industry, they have been used in genetic engineering and pharmaceutical productions (Cohen, Chang, Boyer, & Helling, 1973; Huang, Lin, & Yang, 2012; Kawecki et al., 2013; Lenski, 2004; Schaechter & Neidhardt, 1987). Escherichia coli is a Gram negative bacilli which may possess whip-like flagella for locomotion or hair-like pili for attachment (Blount, 2015). ...
Thesis
A project work submitted to the Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana in partial fulfillment for the award of a BSc degree in Medical Laboratory Science.
... They have been employed in research to study basic life processes such as DNA transcription, translation and replication (Crick, Barnett, Brenner, & Watts-Tobin, 1961;Nirenberg et al., 1965;Judson, 1996). In the industry, they have been used in genetic engineering and pharmaceutical productions (Cohen, Chang, Boyer, & Helling, 1973;Huang, Lin, & Yang, 2012;Kawecki et al., 2013;Lenski, 2004;Schaechter & Neidhardt, 1987). Escherichia coli is a Gram negative bacilli which may possess whip-like flagella for locomotion or hair-like pili for attachment (Blount, 2015). ...
Thesis
A project work submitted to the Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana in partial fulfillment for the award of a BSc degree in Medical Laboratory Science.
... However, most of the cell size reduction is probably an artifact of the experimental design. According to the maximum cell size increases with nutrient availability (because of the uptake kinetics) and should have induced an increase in cell size over time (Lenski 2004). On the other hand cell size and storage capacity are correlated (). ...
Thesis
Full-text available
This Thesis summarizes the adaptive effects of ocean acidification and global warm on the coccolithophore Emiliania huxleyi. The adaptive effects were experimentally assessed in a long term evolutionary experiment. After 2100 asexual generations of selection to CO2 the fitness (growth rate) increased slightly over time under 1100 µatm pCO2. Under 2200 µatm pCO2 the fitness advantage of 5% at 500 generations remained unchanged. The phenotypic trait of calcification was partly restored within 500 generations. Thereafter, calcification was reduced in response to selection. The reduction of calcification was not constitutively, as the calcite per cell quotas were restored when assessed with 400 µatm pCO2. Temperature adaptation occurred independently of ocean acidification levels. The fitness increase in growth rate due was up to 16% in populations adapted to high temperature and high CO2 compared to not adapted cells under selection conditions. The ratio of particular inorganic (PIC) and organic carbon (PIC:POC) recovered to their initial ratio after temperature adaptation, even under elevated CO2. Cells evolved to a smaller size accompanied by a reduction in POC-content. Production rates were restored to values under present-day ocean conditions, owing to adaptive evolution in growth rate. Temperature adaptation increased the effect on persisting CO2 adaptation in growth rate. The immediate physiological effect on PIC per cell was diminished compared to the lower temperature treatment, and so were the adaptive effects. Temperature adaptation reduced the negative effects of ocean acidification. Both adaptations were necessary to receive the full fitness effect under high-temperature-high-CO2-conditions. As consequence both adaptive effects are additive. Global warming may reduce the adverse effects of ocean acidification on E. huxleyi populations. My results show further, that marine phytoplankton may evolve changes in the plastic response under future ocean conditions.
... Another striking feature of Lewontin's, and other formalisations of evolutionary theory, is that the explanatory processes they introduce (like those explaining the origin of variation or heritability) are never described in probabilistic terms. Now, since Williams' and Lewontin's work, the neutralist theory 14 (Kimura 1983), widely accepted by evolutionary biologists, has provided the representation of evolutionary processes with a probabilistic dimension. Taking the probabilistic character of evolutionary processes seriously by representing them with the help of probabilistic laws 15 is the best way to express the explanatory resources of evolutionary theory precisely. ...
Chapter
Full-text available
We propose a formalization of the principles of evolutionary theory as it is currently used in empirical research, in order to enlighten its explanatory resources. We deliberately adopt a minimalist methodology and refuse to include any notion that would not be entirely clear in our formulation. We discuss a few existing formulations and what we see as the touchstone of any formulation of evolutionary theory at the beginning of the twenty-first century: Lenski's experiments on Escherichia coli. We show the conceptual benefits we draw from our formalization
... They have been employed in research to study basic life processes such as DNA transcription, translation and replication (Crick, Barnett, Brenner, & Tobin, 1961; Nirenberg et al., 1965; Judson, 1996). In the industry, they have been used in genetic engineering and pharmaceutical productions (Cohen, Chang, Boyer, & Helling, 1973; Huang, Lin, & Yang, 2012; Kawecki et al., 2013; Lenski, 2004; Schaechter & Neidhardt, 1987). Escherichia coli is a Gram negative bacilli which may possess whip-like flagella for locomotion or hair-like pili for attachment (Blount, 2015). ...
Thesis
A project work submitted to the Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana in partial fulfillment for the award of a BSc degree in Medical Laboratory Science.
... They have been employed in research to study basic life processes such as DNA transcription, translation and replication (Crick, Barnett, Brenner, & Tobin, 1961; Nirenberg et al., 1965; Judson, 1996). In the industry, they have been used in genetic engineering and pharmaceutical productions (Cohen, Chang, Boyer, & Helling, 1973; Huang, Lin, & Yang, 2012; Kawecki et al., 2013; Lenski, 2004; Schaechter & Neidhardt, 1987). Escherichia coli is a Gram negative bacilli which may possess whip-like flagella for locomotion or hair-like pili for attachment (Blount, 2015). ...
Thesis
A project work submitted to the Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana in partial fulfillment for the award of a BSc degree in Medical Laboratory Science.
... In this regard, the failure of the scavenger strain to "take the jump" may be similar to how the long-term evolution of an E. coli strain that can now utilize citrate as a carbon source was confounded by the presence of glucose in the media. 7,8 The modified-indole utilizing strains now lie somewhere in between: they were properly forced to deal with a complete lack of tryptophan, and in consequence began the protein-by-protein modifications necessary to accommodate the new amino acid. It is possible that, were directed evolution to continue in the adapted E. coli strains, the authors might reach the new fitness optimum apparently identified in B. subtilis, where the noncanonical amino acid is favored. ...
Article
Escherichia coli that utilize 4- and 5-fluoroindole and replace tryptophan with fluorinated derivatives throughout their proteomes have been evolved.
... This point is frequently misunderstood, which probably contributes to the confused state of mind of our hypothetical student. For example, retrieving information on the LTEE on Wikipedia (retrieval done on 22 September 2021) states 'By 20 000 generations the populations grew approximately 70% faster than the ancestral strain', citing [13] as the source. The source itself, however, states the exact opposite when being specific about populations being tested separately: 'The evolved populations yield fewer cells than the ancestor when they are grown separately under the standard conditions' [13, p. 245]. ...
Article
Fisher's fundamental theorem states that natural selection improves mean fitness. Fitness, in turn, is often equated with population growth. This leads to an absurd prediction that life evolves to ever-faster growth rates, yet no one seriously claims generally slower population growth rates in the Triassic compared with the present day. I review here, using non-technical language, how fitness can improve yet stay constant (stagnation paradox), and why an unambiguous measure of population fitness does not exist. Subfields use different terminology for aspects of the paradox, referring to stasis, cryptic evolution or the difficulty of choosing an appropriate fitness measure; known resolutions likewise use diverse terms from environmental feedback to density dependence and ‘evolutionary environmental deterioration’. The paradox vanishes when these concepts are understood, and adaptation can lead to declining reproductive output of a population when individuals can improve their fitness by exploiting conspecifics. This is particularly readily observable when males participate in a zero-sum game over paternity and population output depends more strongly on female than male fitness. Even so, the jury is still out regarding the effect of sexual conflict on population fitness. Finally, life-history theory and genetic studies of microevolutionary change could pay more attention to each other.
... Lenski [27] notes that, after 20,000 generations, each of his twelve populations have encountered between 3·10 8 and 1.5 · 10 9 mutations. Therefore, we will use 10 10 as the estimate of the number of mutational events that happened across all twelve populations combined in order to get the potentiating mutation. ...
Article
Full-text available
In computer search optimization theory, active information is a measurement of a search algorithm's internal information as it relates to its problem space. While it has been previously applied to evolutionary search algorithms on computers, it has not been applied yet to biological systems. Active information can be very useful in di erentiating between mutational adaptations which are based on internally-coded information and those which are the results of happenstance. However, biological systems present many practical problems regarding measuring active information which are not present in digital systems. This paper describes active information, how it can be used in biology, and how some of these problems can be overcome in speci c cases.
... Strains were revived overnight in LB then were diluted 10,000-fold into separate cultures for each replicate competition assay in DM containing 25 μg/mL glucose (DM25). These cultures were preconditioned and competed under the same conditions as used in the LTEE [4,40], in 10 mL of DM25 in 50 mL Erlenmeyer flasks shaken at 120 rpm over a diameter of 1 inch with incubation at 37˚C. After 24 h of growth separately to precondition strains to these conditions, two replicate cultures for each Ara − and Ara + pair were mixed at equal volumes in fresh DM25 media such that there was an overall 1:100 dilution. ...
Article
Full-text available
Key innovations are disruptive evolutionary events that enable a species to escape constraints and rapidly diversify. After 15 years of the Lenski long-term evolution experiment with Escherichia coli, cells in one of the twelve populations evolved the ability to utilize citrate, an abundant but previously untapped carbon source in the environment. Descendants of these cells became dominant in the population and subsequently diversified as a consequence of invading this vacant niche. Mutations responsible for the appearance of rudimentary citrate utilization and for refining this ability have been characterized. However, the complete nature of the genetic and/or ecological events that set the stage for this key innovation is unknown. In particular, it is unclear why it took so long for citrate utilization to evolve and why it still has evolved in only one of the twelve E. coli populations after 30 years of the Lenski experiment. In this study, we recapitulated the initial mutation needed to evolve citrate utilization in strains isolated from throughout the first 31,500 generations of the history of this population. We found that there was already a slight fitness benefit for this mutation in the original ancestor of the evolution experiment and in other early isolates. However, evolution of citrate utilization was blocked at this point due to competition with other mutations that improved fitness in the original niche. Subsequently, an anti-potentiated genetic background evolved in which it was deleterious to evolve rudimentary citrate utilization. Only later, after further mutations accumulated that restored the benefit of this first-step mutation and the overall rate of adaptation in the population slowed, was citrate utilization likely to evolve. Thus, intense competition and the types of mutations that it favors can lead to short-sighted evolutionary trajectories that hide a stepping stone needed to access a key innovation from many future generations.
... Experimental evolution using microbes has led to a large number of insights in evolutionary biology [reviewed in Kassen (2014)]. Much of those insights pertain to microbial populations evolving under a single selection pressure which is either static or changing directionally [reviewed in Scheiner (2002) and Lenski (2004)]. However, in nature, multiple selection pressures typically not only operate simultaneously, but also undergo predictable or unpredictable spatiotemporal fluctuations. ...
Article
In nature, organisms are simultaneously exposed to multiple stresses (i.e. complex environments) that often fluctuate unpredictably. While both these factors have been studied in isolation, the interaction of the two remains poorly explored. To address this issue, we selected laboratory populations of Escherichia coli under complex (i.e. stressful combinations of pH, H2 O2 and NaCl) unpredictably fluctuating environments for ~900 generations. We compared the growth rates and the corresponding trade-off patterns of these populations to those that were selected under constant values of the component stresses (i.e. pH, H2 O2 and NaCl) for the same duration. The fluctuation-selected populations had greater mean growth rate and lower variation for growth rate over all the selection environments experienced. However, while the populations selected under constant stresses experienced trade-offs in the environments other than those in which they were selected, the fluctuation-selected populations could by-pass the across-environment trade-offs almost entirely. Interestingly, trade-offs were found between growth rates and carrying capacities. The results suggest that complexity and fluctuations can strongly affect the underlying trade-off structure in evolving populations. This article is protected by copyright. All rights reserved.
... Because many variables can be controlled, this laboratory evolution experiment provides the opportunity to rigorously explore questions pertaining to morphological evolution. The materials and methods that involve the ancestral strain, culture conditions, means for checking contamination, measurement of average cell volume, etc. are demonstrated in the literature (Lenski et al., 1991; Elena and Lenski, 2003; Lenski, 2004). This type of evolution experiment has illustrated more extensive and complicated evolution kinetics than theoretical studies on single populations or alleles. ...
Article
Here, we applied a two-stage clonal expansion model of morphological (cell-size) evolution to a long-term evolution experiment with Escherichia coli. Using this model, we derived the incidence function of the appearance of cell-size stability, the waiting time until this morphological stability, and the conditional and unconditional probabilities of morphological stability. After assessing the parameter values, we verified that the calculated waiting time was consistent with the experimental results, demonstrating the effectiveness of the two-stage model. According to the relative contributions of parameters to the incidence function and the waiting time, cell-size evolution is largely determined by the promotion rate, i.e., the clonal expansion rate of selectively advantageous organisms. This rate plays a prominent role in the evolution of cell size in experimental populations, whereas all other evolutionary forces were found to be less influential.
Article
Full-text available
The topology of fitness landscapes is critical for the efficiency and outcome of natural and directed evolution. Thus far, fitness landscape topology has not been fully characterized due to the enormous size of the sequence space. To meet this challenge, we formulate the physically grounded Optimal landscapes in Evolution (OptiEvo) theory by viewing the particular biological system as (i) interacting with the environment, (ii) utilizing nucleotides as variables, and (iii) optimizing a measure of fitness as the objective. The two basic conclusions of OptiEvo theory are (1) fitness landscapes in a constant homogeneous environment should not contain isolated local peaks (i.e., traps), and (2) the globally optimal genotypes can form a connected level set of equivalent fitness. OptiEvo theory is based on the assumption that biologically realizable gene changes can provide sufficient flexibility to explore the local landscape structure in the process of evolution. Violation of this assumption through restrictions on the gene changes can lead to the presence of local traps on the landscape. A comparison of the biological predictions of OptiEvo with laboratory results in the literature broadly supports the validity of the theory. The predictions of OptiEvo also have implications for the design strategy and outcome of directed evolution experiments. OptiEvo is additionally discussed in the analogous context of recently analyzed fitness landscapes in the chemical and physical sciences.
Article
Evolutionary changes in organismal traits may occur either gradually or suddenly. However, until recently, there has been little direct information about how phenotypic changes are related to the rate and the nature of the underlying genotypic changes. Technological advances that facilitate whole-genome and whole-population sequencing, coupled with experiments that 'watch' evolution in action, have brought new precision to and insights into studies of mutation rates and genome evolution. In this Review, we discuss the evolutionary forces and ecological processes that govern genome dynamics in various laboratory systems in the context of relevant population genetic theory, and we relate these findings to evolution in natural populations.
Article
Full-text available
Evolutionary innovations often arise from complex genetic and ecological interactions, which can make it challenging to understand retrospectively how a novel trait arose. In a long-term experiment, Escherichia coli gained the ability to use abundant citrate (Cit(+)) in the growth medium after ∼31,500 generations of evolution. Exploiting this previously untapped resource was highly beneficial: later Cit(+) variants achieve a much higher population density in this environment. All Cit(+) individuals share a mutation that activates aerobic expression of the citT citrate transporter, but this mutation confers only an extremely weak Cit(+) phenotype on its own. To determine which of the other >70 mutations in early Cit(+) clones were needed to take full advantage of citrate, we developed a recursive genomewide recombination and sequencing method (REGRES) and performed genetic backcrosses to purge mutations not required for Cit(+) from an evolved strain. We discovered a mutation that increased expression of the dctA C4-dicarboxylate transporter greatly enhanced the Cit(+) phenotype after it evolved. Surprisingly, strains containing just the citT and dctA mutations fully use citrate, indicating that earlier mutations thought to have potentiated the initial evolution of Cit(+) are not required for expression of the refined version of this trait. Instead, this metabolic innovation may be contingent on a genetic background, and possibly ecological context, that enabled citT mutants to persist among competitors long enough to obtain dctA or equivalent mutations that conferred an overwhelming advantage. More generally, refinement of an emergent trait from a rudimentary form may be crucial to its evolutionary success.
Conference Paper
Great attentions are still paid to the morphological evolution, such as the waiting time to the morphological stability in constant environment, the contributions of different evolutionary forces to the morphological evolution and so on, despite considerable progress. To investigate these issues, some biologists seek to carry out evolution experiments owing to the incompleteness and uncontrollability of the fossil record and the natural populations. We analyze the morphology (cell size) evolution observed from a long-term evolution experiment with Escherichia coli by Lenski et al. and explore these questions more rigorously. We adopt a population genetics model, the Wright-Fisher model, to describe this morphological evolution and calculate the estimates of the waiting time until the ultimate stasis (near stasis) in morphology (cell size) in the long-term experiment by simulations. These calculations have been verified to be in good accordance with the experimental data, which demonstrates the effectiveness of our model. We have shown how the per-locus mutation rate, the average selection advantage per mutation and the population size devote to the morphology (cell size) evolution. Our results indicate that the selective advantage plays a powerful effect on this morphological evolution. By comparison, the mutation rate and population size have a weaker influence.
Article
Full-text available
Microbial genomes are being extensively studied using next-generation sequencing technologies in order to understand the changes that occur under different selection regimes. In this work, the number and type of mutations that have occurred in three Bradyrhizobium diazoefficiens USDA 110T strains under laboratory conditions and during selection for a more motile phenotypic variant were analyzed. Most of the mutations found in both processes consisted of single nucleotide polymorphisms, single nucleotide deletions or insertions. In the case of adaptation to laboratory conditions, half of the changes occurred within intergenic regions, and around 80% were insertions. When the more motile phenotypic variant was evaluated, eight single nucleotide polymorphisms and an 11-bp deletion were found, although none of them was directly related to known motility or chemotaxis genes. Two mutants were constructed to evaluate the 11-bp deletion affecting the alpha subunit of 2-oxoacid:acceptor oxidoreductase (AAV28_RS30705-blr6743). The results showed that this single deletion was not responsible for the enhanced motility phenotype. IMPORTANCE The genetic and genomic changes that occur under laboratory conditions in Bradyrhizobium diazoefficiens genomes remain poorly studied. Only a few genome sequences of this important nitrogen-fixing species are available, and there are no genome-wide comparative analyses of related strains. In the present work, we sequenced and compared the genomes of strains derived from a parent strain, B. diazoefficiens USDA 110, that has undergone processes of repeated culture in the laboratory environment, or phenotypic selection toward antibiotic resistance and enhanced motility. Our results represent the first analysis in B. diazoefficiens that provides insights into the specific mutations that are acquired during these processes.
Article
Full-text available
Microbes are constantly evolving. Laboratory studies of bacterial evolution increase our understanding of evolutionary dynamics, identify adaptive changes, and answer important questions that impact human health. During bacterial infections in humans, however, the evolutionary parameters acting on infecting populations are likely to be much more complex than those that can be tested in the laboratory. Nonetheless, human infections can be thought of as naturally occurring in vivo bacterial evolution experiments, which can teach us about antibiotic resistance, pathogenesis, and transmission. Here, we review recent advances in the study of within-host bacterial evolution during human infection and discuss practical considerations for conducting such studies. We focus on 2 possible outcomes for de novo adaptive mutations, which we have termed “adapt-and-live” and “adapt-and-die.” In the adapt-and-live scenario, a mutation is long lived, enabling its transmission on to other individuals, or the establishment of chronic infection. In the adapt-and-die scenario, a mutation is rapidly extinguished, either because it carries a substantial fitness cost, it arises within tissues that block transmission to new hosts, it is outcompeted by more fit clones, or the infection resolves. Adapt-and-die mutations can provide rich information about selection pressures in vivo, yet they can easily elude detection because they are short lived, may be more difficult to sample, or could be maladaptive in the long term. Understanding how bacteria adapt under each of these scenarios can reveal new insights about the basic biology of pathogenic microbes and could aid in the design of new translational approaches to combat bacterial infections.
Thesis
Full-text available
The importance of historical contingency in evolution has been extensively debated over the last few decades, but direct empirical tests have been rare. Twelve initially identical populations of E. coli were founded in 1988 to investigate this issue. They have since evolved for more than 50,000 generations in a glucose-limited medium that also contains a citrate. However, the inability to use citrate as a carbon source under oxic conditions is a species-defining trait of E. coli. A weakly Cit+ variant capable of aerobic citrate utilization finally evolved in one population just prior to 31,500 generations. Shortly after 33,000 generations, the population experienced a several-fold expansion as strongly Cit+ variants rose to numerical dominance (but not fixation). The Cit+ trait was therefore a key innovation that increased both population size and diversity by opening a previously unexploited ecological opportunity. The long-delayed and unique evolution of the Cit+ innovation might be explained by two possible hypotheses. First, evolution of the Cit+ function may have required an extremely rare mutation. Alternately, the evolution of Cit+ may have been contingent upon one or more earlier mutations that had accrued over the population’s history. I tested these hypotheses in a series of experiments in which I “replayed” evolution from different points in the population’s history. I observed no Cit+ mutants among 8.4 x 1012 ancestral cells, nor among 9 x 1012 cells from 60 clones sampled in the first 15,000 generations. However, I observed a significantly greater tendency to evolve Cit+ among later clones. These results indicate that one or more earlier mutations potentiated the evolution of Cit+ by increasing the rate of mutation to Cit+ to an accessible, though still very low, level. The evolution of the Cit+ function was therefore contingent on the particular history of the population in which it occurred. I investigated the Cit+ innovation’s history and genetic basis by sequencing the genomes of 29 clones isolated from the population at various time points. Analysis of these genomes revealed that at least 3 distinct clades coexisted for more than 10,000 generations prior to the innovation’s evolution. The Cit+ trait originated in one clade by a tandem duplication that produced a new regulatory module in which a silent citrate transporter was placed under the control of an aerobically-expressed promoter. Subsequent increases in the copy number of this new regulatory module refined the initially weak Cit+ phenotype, leading to the population expansion. The 3 clades varied in their propensity to evolve the novel Cit+ function, though genotypes able to do so existed in all 3, implying that potentiation involved multiple mutations. My findings demonstrate that historical contingency can significantly impact evolution, even under the strictest of conditions. Moreover, they suggest that contingency plays an especially important role in the evolution of novel innovations that, like Cit+, require prior construction of a potentiating genetic background, and are thus not easily evolved by gradual, cumulative selection. Contingency may therefore have profoundly shaped life’s evolution given the importance of evolutionary novelties in the history of life. Finally, the genetic basis of the Cit+ function illustrates the importance of promoter capture and altered gene regulation in mediation the exaptation events that often underlie evolutionary innovations.
Article
Twelve replicate populations of Escherichia coli have been evolving in the laboratory for more than 25 years and 60,000 generations. We analyzed bacteria from whole-population samples frozen every 500 generations through 20,000 generations for one well-studied population, called Ara-1. By tracking 42 known mutations in these samples, we reconstructed the history of this population's genotypic evolution over this period. The evolutionary dynamics of Ara-1 show strong evidence of selective sweeps as well as clonal interference between competing lineages bearing different beneficial mutations. In some cases, sets of several mutations approached fixation simultaneously, often conveying no information about their order of origination; we present several possible explanations for the existence of these mutational cohorts. Against a backdrop of rapid selective sweeps both earlier and later, two genetically diverged clades coexisted for over 6000 generations before one went extinct. In that time, many additional mutations arose in the clade that eventually prevailed. We show that the clades evolved a frequency-dependent interaction, which prevented the immediate competitive exclusion of either clade, but which collapsed as beneficial mutations accumulated in the clade that prevailed. Clonal interference and frequency dependence can occur even in the simplest microbial populations. Furthermore, frequency dependence may generate dynamics that extend the period of coexistence that would otherwise be sustained by clonal interference alone. Copyright © 2015, The Genetics Society of America.
Thesis
Full-text available
Frankia est une actinobactérie capable d'établir une symbiose racinaire avec les plantes actinorhiziennes dont le genre Alnus. Seulement certaines souches de Frankia sont capables de sporuler in planta, ce qui est illustré par la présence (Sp+) ou l'absence (Sp–) de sporanges dans les cellules végétales de la nodosité. C’est à notre connaissance un cas unique de sporulation endophyte. Cependant la description et l’interprétation écologique de ce trait d’histoire de vie (THV) original étaient incomplètes. Notre contribution à l’étude de la sporulation in planta des Frankia infectives de l’aulne intègre des approches théorique, descriptive et expérimentale, pour préciser (i) l’influence relative de la souche bactérienne, de l’espèce de la plante-hôte et des conditions pédoclimatiques sur ce THV, (ii) le rôle de la variabilité environnementale sur la distribution, la diversité et la sélection du trait, ainsi que (iii) les coûts et bénéfices associés pour les deux partenaires. Nous avons démontré pour la première fois que la sporulation in planta est un THV (i) spécifique de certaines lignées de Frankia, (ii) majeur pour en comprendre l'histoire évolutive et (iii) significativement corrélé à des caractéristiques génétiques des souches. Nous avons également confirmé que l’occurrence du trait varie selon l’environnement. Nous avons enfin établi un modèle de l'évolution du trait abordant sa valeur adaptative. L’ensemble des réflexions menées et des résultats obtenus nous permet de discuter de la sporulation in planta dans le cadre d’un continuum de stratégies symbiotiques, et plus généralement de discuter de l’écologie évolutive des symbioses entre microorganismes et plantes
Preprint
Full-text available
After 15 years of the Lenski experiment one of twelve Escherichia coli populations evolved the ability to utilize an abundant but previously untapped carbon source, citrate. Mutations responsible for the appearance of rudimentary citrate utilization (Cit ⁺ phenotype) and for refining this ability have been characterized. However, the complete nature of the genetic and/or ecological events that set the stage for this key innovation remain unknown. We found that there was a slight fitness benefit for introducing an activated citT cassette that mimics the mutation causing Cit ⁺ into the ancestor of the evolution experiment and strains isolated from the population close to when it evolved. However, there was no benefit or even a large deleterious effect in intermediate strains. We conclude that achieving Cit ⁺ was contingent on both an evolutionary trajectory that maintained a potentiated genetic state and the slowing rate of adaptation in this population late in the experiment.
Article
Full-text available
Levy flights in the space of mutations model time evolution of bacterial DNA. Parameters in the model are adjusted in order to fit observations coming from the Long Time Evolution Experiment with E. Coli.
Article
Full-text available
Along an individual lifetime, stem cells replicate and suffer modifications in their DNA content. I model the modifications in the DNA of a single cell as Levy flights, made up of small amplitude Brownian motions plus rare large-jumps events. The distribution function of mutations has a long tail, in which cancer events are located far away. The probability of cancer in a given tissue is roughly estimated as a Ncell Nstep, where Ncell is the number of stem cells, and Nstep -- the number of replication steps in the evolution of a single cell. I test this expression against recent data on lifetime cancer risk, Ncell and Nstep in different tissues. The coefficient a takes values between 2x10^{-15} and 2x10^{-11}, depending on the role played by carcinogenic factors and the immune response. The smallest values of a correspond to cancers in which randomness plays the major role.
Chapter
The concept of a landscape or response surface naturally arises in applications widely ranging over the sciences, engineering and other disciplines. A landscape is the desired output as a function of a set of input variables, often of very high dimension. The relationship between the features of a landscape and the input variables is usually unknown a priori and often thought to be highly complex due to the anticipated intricate interactions involved. This chapter reviews recent developments in the analysis of landscape topology with the input variables considered as controls. Taking a control perspective allows for the specification of particular assumptions whose satisfaction permits a general analysis of the landscape topology. Satisfaction of these conditions leads to the conclusion that control landscapes should be devoid of suboptimal critical point traps, thereby permitting ready excursions without hindrance to the highest values of the landscape. These principles are set out in a general framework and then specifically illustrated for applications involving control in quantum mechanics, chemical and material science, and in natural and directed evolution. Perspectives are given on the significance of these findings and potential future directions for additional analysis of landscape principles.
Article
We propose a formalization of the principles of evolutionary theory as it is currently used in empirical research, in order to enlighten its explanatory resources. We deliberately adopt a minimalist methodology and refuse to include any notion that would not be entirely clear in our formulation. We discuss a few existing formulations and what we see as the touchstone of any formulation of evolutionary theory at the beginning of the twenty-first century: Lenski's experiments on Escherichia coli. We show the conceptual benefits we draw from our formalization.
Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history of its own. The degree to which these characteristics render evolution historically contingent, and evolutionary outcomes thereby unpredictably sensitive to history has been the subject of considerable debate in recent decades. Microbial evolution experiments have proven among the most fruitful means of empirically investigating the issue of historical contingency in evolution. One such experiment is the E. coli Long-Term Evolution Experiment (LTEE), in which twelve populations founded from the same clone of E. coli have evolved in parallel under identical conditions. Aerobic growth on citrate (Cit+), a novel trait for E. coli, evolved in one of these populations after more than 30,000 generations. Experimental replays of this population’s evolution from various points in its history showed that the Cit+ trait was historically contingent upon earlier mutations that potentiated the trait by rendering it mutationally accessible. Here I review this case of evolutionary contingency and discuss what it implies about the importance of historical contingency arising from the core processes of evolution.
Article
Full-text available
The increasing maximal hierarchical complexity of organisms is one of the best-supported macroevolutionary trends. The nature and causes of this trend, as well as several accompanying macroevolutionary phenomena are, however, still unclear. In this theoretical article, we propose that the cause of this trend could be the increasing pressure of species selection, which results from the gradual decrease of (macro)evolutionary potential (i.e. the probability of producing major evolutionary innovations). As follows from the Theory of Frozen Evolution, this process is an inevitable consequence of the sorting of genes, traits, and their integrated groups (modules) based on their contextually dependent stability. In turn, this causes effectively unchangeable elements of genetic architecture to accumulate during the existence of evolutionary lineages. Although (macro)evolutionary potential can be partially restored by several processes, a profound restoration of (macro)evolutionary potential is probably possible only by means of a transition to a higher level of hierarchical complexity. However, the accumulation of contextually more stable elements continues even on this higher level. This leads to the integration of the modular character of composite organisms and a repeated pressure to increase the level of hierarchical complexity. Our model explains all components of McShea’s “Evolutionary Syndrome,” i.e. the trend of increasing the hierarchical complexity of organisms, the growth of variability among elements on the immediately lower level, and their gradual machinification. This pattern should be characteristic of sexual eukaryotes and especially their complex representatives. Our model also sheds new light on several related macroevolutionary phenomena, such as the gradual acceleration of the trend or the striking difference between pre-Neoproterozoic and Phanerozoic evolution.
Article
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
Article
Full-text available
Cost effective and scalable methods for phage production are required to meet an increasing demand for phage, as an alternative to antibiotics. Computational models can assist the optimization of such production processes. A model is developed here that can simulate the dynamics of phage population growth and production in a two-stage, self-cycling process. The model incorporates variable infection parameters as a function of bacterial growth rate and employs ordinary differential equations, allowing application to a setup with multiple reactors. The model provides simple cost estimates as a function of key operational parameters including substrate concentration, feed volume and cycling times. For the phage and bacteria pairing examined, costs and productivity varied by three orders of magnitude, with the lowest cost found to be most sensitive to the influent substrate concentration and low level setting in the first vessel. An example case study of phage production is also presented, showing how parameter values affect the production costs and estimating production times. The approach presented is flexible and can be used to optimize phage production at laboratory or factory scale by minimizing costs or maximizing productivity.
Article
In the past three decades laboratory natural selection has become a widely used technique in biological research. Most studies which have utilized this technique are in the realm of basic science, often testing hypotheses related to mechanisms of evolutionary change or ecological dynamics. While laboratory natural selection is currently utilized heavily in this setting, there is a significant gap with its usage in applied studies, especially when compared to the other selection experiment methodologies like artificial selection and directed evolution. This is despite avenues of research in the applied sciences which seem well suited to laboratory natural selection. In this commentary we place laboratory natural selection in context with other selection experiments, identify the characteristics which make it well suited for particular kinds of applied research, and briefly cover key examples of the usefulness of selection experiments within applied science. Finally, we identify three promising areas of inquiry for laboratory natural selection in the applied sciences: bioremediation technology, identifying mechanisms of drug resistance, and optimizing biofuel production. Although laboratory natural selection is currently less utilized in applied science when compared to basic research, the method has immense promise in the field moving forward.
Thesis
Full-text available
Frankia sp. is a telluric actinobacteria able to establish a root symbiosis with actinorhizal plant such as Alnus sp. Only some Frankia strains are able to sporulate in-planta, as spores can be present in (Sp+) or absent from (Sp–) the vegetal cells of the root nodule. It is to our knowledge a unique case of endophytic sporulation. However, the description and the ecological interpretation of this original life-history trait (LHT) were scarce. Our contribution to the studyofthein-plantasporulationofAlnus-infective Frankia sp. combines theoretical, descriptive and experimental approaches to precise (i) the relative effect of the bacterial strain, the host-plant species and the pedoclimatic conditions on this LHT, (ii) the effect of the of the environmental variability on the distribution, diversity and selection of the trait, and (iii) the associated costs and benefits for the two symbiotic partners. We demonstrated for the first time that the in-planta sporulation is a LHT (i) specific to some Frankia lineages, (ii) major to understand their evolutionary history and (iii) significantly correlated to particular genetic features. We also shown that the occurrence of the trait varies according to the environment We also proposed a model of the evolution of the trait taking its fitness into account. We bring all the previous considerations and results to discuss the in- planta sporulation trait within a continuum of symbiotic strategies and more generally to discuss the evolutionary ecology of plant-microbe symbioses.
Article
Full-text available
Fungicide resistance is a constant threat to agricultural production worldwide. Molecular mechanisms of fungicide resistance have been studied extensively in the wheat pathogen Zymoseptoria tritici. However, less is known about the evolutionary processes driving resistance development. In vitro evolutionary studies give the opportunity to investigate this. Here, we examine the adaptation of Z. tritici to fluxapyroxad, a succinate dehydrogenase (Sdh) inhibitor. Replicate populations of Z. tritici derived from the sensitive isolate IPO323 were exposed to increasing concentrations of fluxapyroxad with or without UV mutagenesis. After ten increases in fungicide concentration, sensitivity had decreased dramatically, with replicate populations showing similar phenotypic trajectories. Sequencing the Sdh subunit B, C and D encoding genes identified seven mutations associated with resistance to fluxapyroxad. Mutation frequency over time was measured with a pyrosequencing assay, revealing sequential lineage replacement in the UV mutagenized populations but not in the untreated populations. Repeating selection from set time-points with different fungicide concentrations revealed that haplotype replacement of Sdh variants was driven by dose-dependent selection as fungicide concentration changed, and was not mutation-limited. These findings suggest that fungicide field applications may select for highly insensitive Sdh variants with higher resistance factors if the fungicide concentration is increased to achieve a better disease control. However, in the absence or presence of lower fungicide concentrations, the spread of these strains might be restricted if the underlying Sdh mutations carry fitness penalties. This article is protected by copyright. All rights reserved.
Article
Full-text available
EPSP synthase is the target enzyme of glyphosate herbicides. Due to the extensive use of glyphosate, it is very important to obtain EPSPS genes with high glyphosate resistance for the development of transgenic crops. GR79-EPSPS is a class I EPSP synthase with certain glyphosate resistance isolated from glyphosate-contaminated soil. After more than 1000 generations, a Y40I substitution was identified, and the enzyme had a nearly 1.8-fold decrease in Km [PEP] and a 1.7-fold increase in Ki[glyphosate] compared to the wild-type enzyme. Enzyme dynamics and molecular dynamics analysis showed that the substitution was near the hinge region of EPSPS, and the affinity of glyphosate binding to amino acid residues of the active site decreased due to Y40I substitution, resulting in an increase in glyphosate resistance. These results provide more evidence for the combination of directed evolution and rational design of protein engineering.
Article
Full-text available
Twelve populations of the bacterium Escherichia coli were propagated for 2,000 generations in a seasonal environment, which consisted of alternating periods of feast and famine. The mean fitness of the derived genotypes increased by approximately 35% relative to their common ancestor, based on competition experiments in the same environment. The bacteria could have adapted, in principle, by decreasing their lag prior to growth upon transfer to fresh medium (L), increasing their maximum growth rate (V(m)), reducing the the concentration of resource required to support growth at half the maximum rate (K(s)), and reducing their death rate after the limiting resource was exhausted (D). We estimated these parameters for the ancestor and then calculated the opportunity for selection on each parameter. The inferred selection gradients for V(m) and L were much steeper than for K(s) and D. The derived genotypes showed significant improvement in V(m) and L but not in K(s) or D. Also, the numerical yield in pure culture of the derived genotypes was significantly lower than the yield of the common ancestor, but the average cell size was much larger. The independently derived genotypes are somewhat more variable in these life-history traits than in their relative fitnesses, which indicates that they acquired different genetic adaptations to the seasonal environment. Nonetheless, the evolutionary changes in life-history traits exhibit substantial parallelism among the replicate populations.
Article
Full-text available
An important problem in microbial ecology is to identify those phenotypic attributes that are responsible for competitive fitness in a particular environment. Thousands of papers have been published on the physiology, biochemistry, and molecular genetics of Escherichia coli and other bacterial models. Nonetheless, little is known about what makes one genotype a better competitor than another even in such well studied systems. Here, we review experiments to identify the phenotypic bases of improved competitive fitness in twelve E. coli populations that evolved for thousands of generations in a defined environment, in which glucose was the limiting substrate. After 10000 generations, the average fitness of the derived genotypes had increased by 50% relative to the ancestor, based on competition experiments using marked strains in the same environment. The growth kinetics of the ancestral and derived genotypes showed that the latter have a shorter lag phase upon transfer into fresh medium and a higher maximum growth rate. Competition experiments were also performed in environments where other substrates were substituted for glucose. The derived genotypes are generally more fit in competition for those substrates that use the same mechanism of transport as glucose, which suggests that enhanced transport was an important target of natural selection in the evolutionary environment. All of the derived genotypes produce much larger cells than does the ancestor, even when both types are forced to grow at the same rate. Some, but not all, of the derived genotypes also have greatly elevated mutation rates. Efforts are now underway to identify the genetic changes that underlie those phenotypic changes, especially substrate specificity and elevated mutation rate, for which there are good candidate loci. Identification and subsequent manipulation of these genes may provide new insights into the reproducibility of adaptive evolution, the importance of co-adapted gene complexes, and the extent to which distinct phenotypes (e.g., substrate specificity and cell size) are affected by the same mutations.
Article
Full-text available
We followed evolutionary change in 12 populations of Escherichia coli propagated for 10,000 generations in identical environments. Both morphology (cell size) and fitness (measured in competition with the ancestor) evolved rapidly for the first 2000 generations or so after the populations were introduced into the experimental environment, but both were nearly static for the last 5000 generations. Although evolving in identical environments, the replicate populations diverged significantly from one another in both morphology and mean fitness. The divergence in mean fitness was sustained and implies that the populations have approached different fitness peaks of unequal height in the adaptive landscape. Although the experimental time scale and environment were microevolutionary in scope, our experiments were designed to address questions concerning the origin as well as the fate of genetic and phenotypic novelties, the repeatability of adaptation, the diversification of lineages, and thus the causes and consequences of the uniqueness of evolutionary history. In fact, we observed several hallmarks of macroevolutionary dynamics, including periods of rapid evolution and stasis, altered functional relationships between traits, and concordance of anagenetic and cladogenetic trends. Our results support a Wrightian interpretation, in which chance events (mutation and drift) play an important role in adaptive evolution, as do the complex genetic interactions that underlie the structure of organisms.
Article
Full-text available
Mutations are a double-edged sword: they are the ultimate source of genetic variation upon which evolution depends, yet most mutations affecting fitness (viability and reproductive success) appear to be harmful. Deleterious mutations of small effect can escape natural selection, and should accumulate in small population. Reduced fitness from deleterious-mutation accumulation may be important in the evolution of sex, mate choice, and diploid life-cycles, and in the extinction of small populations. Few empirical data exist, however. Minimum estimates of the genomic deleterious-mutation rate for viability in Drosophila melanogaster are surprisingly high, leading to the conjecture that the rate for total fitness could exceed 1.0 mutation per individual per generation. Here we use Escherichia coli to provide an estimate of the genomic deleterious-mutation rate for total fitness in a microbe. We estimate that the per-microbe rate of deleterious mutations is in excess of 0.0002.
Article
Full-text available
For more than two decades there has been intense debate over the hypothesis that most morphological evolution occurs during relatively brief episodes of rapid change that punctuate much longer periods of stasis. A clear and unambiguous case of punctuated evolution is presented for cell size in a population of Escherichia coli evolving for 3000 generations in a constant environment. The punctuation is caused by natural selection as rare, beneficial mutations sweep successively through the population. This experiment shows that the most elementary processes in population genetics can give rise to punctuated evolutionary dynamics.
Article
Full-text available
This study investigates the physiological manifestation of adaptive evolutionary change in 12 replicate populations of Escherichia coli that were propagated for 2000 generations in a glucose-limited environment. Representative genotypes from each population were assayed for fitness relative to their common ancestor in the experimental glucose environment and in 11 novel single-nutrient environments. After 2000 generations, the 12 derived genotypes had diverged into at least six distinct phenotypic classes. The nutrients were classified into four groups based upon their uptake physiology. All 12 derived genotypes improved in fitness by similar amounts in the glucose environment, and this pattern of parallel fitness gains was also seen in those novel environments where the limiting nutrient shared uptake mechanisms with glucose. Fitness showed little or no consistent improvement, but much greater genetic variation, in novel environments where the limiting nutrient differed from glucose in its uptake mechanisms. This pattern of fitness variation in the novel nutrient environments suggests that the independently derived genotypes adapted to the glucose environment by similar, but not identical, changes in the physiological mechanisms for moving glucose across both the inner and outer membranes.
Article
Full-text available
Populations of Escherichia coli that have been serially propagated for thousands of generations in glucose minimal medium show heritable increases in both cell size and growth rate. We sought to test the hypothesis that the increased cell size of the derived genotypes could be explained solely by their faster growth. The regression of cell size on growth rate differed significantly between populations having ancestral and derived genotypes, with the latter producing larger cells over almost the entire range of growth rates. Thus, the physiological coupling between cell size and growth rate has been evolutionarily altered.
Article
Full-text available
Most mutations are likely to be deleterious, and so the spontaneous mutation rate is generally held at a very low value. Nonetheless, evolutionary theory predicts that high mutation rates can evolve under certain circumstances. Empirical observations have previously been limited to short-term studies of the fates of mutator strains deliberately introduced into laboratory populations of Escherichia coli, and to the effects of intense selective events on mutator frequencies in E. coli. Here we report the rise of spontaneously originated mutators in populations of E. coli undergoing long-term adaptation to a new environment. Our results corroborate computer simulations of mutator evolution in adapting clonal populations, and may help to explain observations that associate high mutation rates with emerging pathogens and with certain cancers.
Article
Full-text available
Because most newly arising mutations are neutral or deleterious, it has been argued that the mutation rate has evolved to be as low as possible, limited only by the cost of error-avoidance and error-correction mechanisms. But up to one per cent of natural bacterial isolates are 'mutator' clones that have high mutation rates. We consider here whether high mutation rates might play an important role in adaptive evolution. Models of large, asexual, clonal populations adapting to a new environment show that strong mutator genes (such as those that increase mutation rates by 1,000-fold) can accelerate adaptation, even if the mutator gene remains at a very low frequency (for example, 10[-5]). Less potent mutators (10 to 100-fold increase) can become fixed in a fraction of finite populations. The parameters of the model have been set to values typical for Escherichia coli cultures, which behave in a manner similar to the model in long-term adaptation experiments.
Article
Full-text available
The 4,639,221–base pair sequence of Escherichia coliK-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.
Article
Full-text available
In sexual populations, beneficial mutations that occur in different lineages may be recombined into a single lineage. In asexual populations, however, clones that carry such alternative beneficial mutations compete with one another and, thereby, interfere with the expected progression of a given mutation to fixation. From theoretical exploration of such 'clonal interference', we have derived (1) a fixation probability for beneficial mutations, (2) an expected substitution rate, (3) an expected coefficient of selection for realized substitutions, (4) an expected rate of fitness increase, (5) the probability that a beneficial mutation transiently achieves polymorphic frequency (> or = 1%), and (6) the probability that a beneficial mutation transiently achieves majority status. Based on (2) and (3), we were able to estimate the beneficial mutation rate and the distribution of mutational effects from changes in mean fitness in an evolving E. coli population.
Article
Full-text available
Mutator genotypes with increased mutation rates may be especially important in microbial evolution if genetic adaptation is generally limited by the supply of mutations. In experimental populations of the bacterium Escherichia coli, the rate of evolutionary adaptation was proportional to the mutation supply rate only in particular circumstances of small or initially well-adapted populations. These experiments also demonstrate a "speed limit" on adaptive evolution in asexual populations, one that is independent of the mutation supply rate.
Article
Full-text available
Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief.
Article
Full-text available
Attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few bacterial taxa for which ancestors can be reliably dated from ecological or geological evidence. Despite similarities in the substitution rates estimated for some lineages, comparisons of the relative rates of evolution at different classes of nucleotide sites indicate no basis for their universal application to all bacteria. However, there is evidence that bacteria have a constant genome-wide mutation rate on an evolutionary time scale but that this rate differs dramatically from the rate estimated by experimental methods.
Article
Full-text available
We describe the short- and long-term dynamics of a phenotypic polymorphism that arose in a population of Escherichia coli while it was serially propagated for almost 20,000 generations in a glucose-limited minimal medium. The two types, designated L and S, differ conspicuously in the size of the colonies they form on agar plates as well as the size of their individual cells, and these differences are heritable. The S type reached a detectable frequency (>1%) at generation 6,000, and it remained above that frequency throughout the subsequent generations. In addition to morphological differences, L and S diverged in important ecological properties. With clones isolated at 18,000 generations, L has a maximal growth rate in fresh medium that is approximately 20% higher than that of S. However, experiments with conditioned media demonstrate that L and S secrete one or more metabolites that promote the growth of S but not of L. The death rate of L during stationary phase also increases when S is abundant, which suggests that S may either secrete a metabolite that is toxic to L or remove some factor that enables the survival of L. One-day competition experiments with the clones isolated at generation 18,000 show that their relative fitness is frequency dependent, with each type having an advantage when rare. When these two types are grown together for a period of several weeks, they converge on an equilibrium frequency that is consistent with the 1-d competition experiments. Over the entire 14,000-generation period of coexistence, however, the frequency of the S type fluctuated between approximately 10% and 85%. We offer several hypotheses that may explain the fluctuations in this balanced polymorphism, including the possibility of coevolution between the two types.
Article
Full-text available
We have examined the composition of members of mutator populations of Escherichia coli by employing an extensive set of phenotypic screens that allow us to monitor the function of >700 genes, constituting approximately 15% of the genome. We looked at mismatch repair deficient cells after repeated cycles of single colony isolation on rich medium to generate lineages that are forced through severe bottlenecks, and compared the results to those for wild-type strains. The mutator lineages continued to accumulate mutations rapidly with each increasing cycle of colony isolation. By the end of the 40th cycle, after approximately 1000 generations, most of the lineages had reduced colony size, 4% had died out, 55% had auxotrophic requirements (increasing to 80% after 60 cycles), and 70% had defects in at least one sugar or catabolic pathway. In addition, 33% had a defect in cell motility, and 26% were either temperature-sensitive or cold-sensitive lethals. On the other hand, only 3% of the wild-type lineages had detectable mutations of any type after 40 cycles. By the 60th cycle, the typical mutator cell carried 4-5 inactive genes among the 15% of the genome being monitored, indicating that the average cell carried at least 24-30 inactivated genes distributed throughout the genome. Remarkably, 30% of the lineages had lost the ability to utilize xylose as a carbon source. DNA sequencing revealed that most of the Xyl(-) mutants had a frameshift in a run of eight G's (GGGGGGGG) in the xylB gene, either adding or deleting one -G-. Further analysis indicated that rendering E. coli deficient in mismatch repair unmasks hypermutable sites in certain genes or intergenic regions. Growth curves and competition tests on lineages that passed through 90 cycles of single colony isolation showed that all lineages suffered reduced fitness. We discuss these results in terms of the value of mutators in cellular evolution.
Article
Full-text available
As part of a long-term evolution experiment, two populations of Escherichia coli B adapted to a glucose minimal medium for 10,000 generations. In both populations, multiple IS-associated mutations arose that then went to fixation. We identify the affected genetic loci and characterize the molecular events that produced nine of these mutations. All nine were IS-mediated events, including simple insertions as well as recombination between homologous elements that generated inversions and deletions. Sequencing DNA adjacent to the insertions indicates that the affected genes are involved in central metabolism (knockouts of pykF and nadR), cell wall synthesis (adjacent to the promoter of pbpA-rodA), and ill-defined functions (knockouts of hokB-sokB and yfcU). These genes are candidates for manipulation and competition experiments to determine whether the mutations were beneficial or merely hitchhiked to fixation.
Article
Full-text available
When organisms adapt genetically to one environment, they may lose fitness in other environments. Two distinct population genetic processes can produce ecological specialization-mutation accumulation and antagonistic pleiotropy. In mutation accumulation, mutations become fixed by genetic drift in genes that are not maintained by selection; adaptation to one environment and loss of adaptation to another are caused by different mutations. Antagonistic pleiotropy arises from trade-offs, such that the same mutations that are beneficial in one environment are detrimental in another. In general, it is difficult to distinguish between these processes. We analysed the decay of unused catabolic functions in 12 lines of Escherichia coli propagated on glucose for 20,000 generations. During that time, several lines evolved high mutation rates. If mutation accumulation is important, their unused functions should decay more than the other lines, but no significant difference was observed. Moreover, most catabolic losses occurred early in the experiment when beneficial mutations were being rapidly fixed, a pattern predicted by antagonistic pleiotropy. Thus, antagonistic pleiotropy appears more important than mutation accumulation for the decay of unused catabolic functions in these populations.
Article
Full-text available
Twelve populations of Escherichia coli B all lostd-ribose catabolic function during 2,000 generations of evolution in glucose minimal medium. We sought to identify the population genetic processes and molecular genetic events that caused these rapid and parallel losses. Seven independent Rbs−mutants were isolated, and their competitive fitnesses were measured relative to that of their Rbs+ progenitor. These Rbs− mutants were all about 1 to 2% more fit than the progenitor. A fluctuation test revealed an unusually high rate, about 5 × 10−5 per cell generation, of mutation from Rbs+ to Rbs−, which contributed to rapid fixation. At the molecular level, the loss of ribose catabolic function involved the deletion of part or all of the ribose operon (rbs genes). The physical extent of the deletion varied between mutants, but each deletion was associated with an IS150 element located immediately upstream of therbs operon. The deletions apparently involved transposition into various locations within the rbs operon; recombination between the new IS150 copy and the one upstream of therbs operon then led to the deletion of the intervening sequence. To confirm that the beneficial fitness effect was caused by deletion of the rbs operon (and not some undetected mutation elsewhere), we used P1 transduction to restore the functionalrbs operon to two Rbs− mutants, and we constructed another Rbs− strain by gene replacement with a deletion not involving IS150. All three of these new constructs confirmed that Rbs− mutants have a competitive advantage relative to their Rbs+ counterparts in glucose minimal medium. The rapid and parallel evolutionary losses of ribose catabolic function thus involved both (i) an unusually high mutation rate, such that Rbs− mutants appeared repeatedly in all populations, and (ii) a selective advantage in glucose minimal medium that drove these mutants to fixation.
Article
Full-text available
Laboratory experiments under controlled conditions during thousands of generations are useful tools to assess the processes underlying bacterial evolution. As a result of these experiments, the way in which the traits change in time is obtained. Under these conditions, the bacteria E. coli shows a parallel increase in cell volume and fitness. To explain this pattern it is required to consider organismic and population contributions. For this purpose we incorporate relevant information concerning bacterial structure, composition and transformations in a minimal modular model. In the short time scale, the model reproduces the physiological responses of the traits to changes in nutrient concentration. The decay of unused catabolic functions, found experimentally, is introduced in the model using simple population genetics. The resulting curves representing the evolution of volume and fitness in time are in good agreement with those obtained experimentally. This study draws attention on physiology when studying evolution. Moreover, minimal modular models appear to be an adequate strategy to unite these barely related disciplines of biology.
Article
Full-text available
Experimental populations of Escherichia coli have evolved for 20,000 generations in a uniform environment. Their rate of improvement, as measured in competitions with the ancestor in that environment, has declined substantially over this period. This deceleration has been interpreted as the bacteria approaching a peak or plateau in a fitness landscape. Alternatively, this deceleration might be caused by non-transitive competitive interactions, in particular such that the measured advantage of later genotypes relative to earlier ones would be greater if they competed directly. To distinguish these two hypotheses, we performed a large set of competitions using one of the evolved lines. Twenty-one samples obtained at 1,000-generation intervals each competed against five genetically marked clones isolated at 5,000-generation intervals, with three-fold replication. The pattern of relative fitness values for these 315 pairwise competitions was compared with expectations under transitive and non-transitive models, the latter structured to produce the observed deceleration in fitness relative to the ancestor. In general, the relative fitness of later and earlier generations measured by direct competition agrees well with the fitness inferred from separately competing each against the ancestor. These data thus support the transitive model. Non-transitive competitive interactions were not a major feature of evolution in this population. Instead, the pronounced deceleration in its rate of fitness improvement indicates that the population early on incorporated most of those mutations that provided the greatest gains, and subsequently relied on beneficial mutations that were fewer in number, smaller in effect, or both.
Article
Full-text available
We examined rates of DNA sequence evolution in 12 populations of Escherichia coli propagated in a glucose minimal medium for 20,000 generations. Previous work saw mutations mediated by mobile elements in these populations, but the extent of other genomic changes was not investigated. Four of the populations evolved defects in DNA repair and became mutators. Some 500 bp was sequenced in each of 36 genes for 50 clones, including 2 ancestral variants, 2 clones from each population at generation 10,000, and 2 from each at generation 20,000. Ten mutations were found in total, all point mutations including mostly synonymous substitutions and nonsynonymous polymorphisms; all 10 were found in mutator populations. We compared the observed sequence evolution to predictions based on different scenarios. The number of synonymous substitutions is lower than predicted from measured mutation rates in E. coli, but the number is higher than rates based on comparing E. coli and Salmonella genomes. Extrapolating to the entire genome, these data predict about 250 synonymous substitutions on average per mutator population, but only about 3 synonymous substitutions per nonmutator population, during 20,000 generations. These data illustrate the challenge of finding sequence variation among bacterial isolates that share such a recent ancestor. However, this limited variation also provides a useful baseline for research aimed at finding the beneficial substitutions in these populations.
Article
Full-text available
Twelve populations of Escherichia coli, derived from a common ancestor, evolved in a glucose-limited medium for 20,000 generations. Here we use DNA expression arrays to examine whether gene-expression profiles in two populations evolved in parallel, which would indicate adaptation, and to gain insight into the mechanisms underlying their adaptation. We compared the expression profile of the ancestor to that of clones sampled from both populations after 20,000 generations. The expression of 59 genes had changed significantly in both populations. Remarkably, all 59 were changed in the same direction relative to the ancestor. Many of these genes were members of the cAMP-cAMP receptor protein (CRP) and guanosine tetraphosphate (ppGpp) regulons. Sequencing of several genes controlling the effectors of these regulons found a nonsynonymous mutation in spoT in one population. Moving this mutation into the ancestral background showed that it increased fitness and produced many of the expression changes manifest after 20,000 generations. The same mutation had no effect on fitness when introduced into the other evolved population, indicating that a mutation of similar effect was present already. Our study demonstrates the utility of expression arrays for addressing evolutionary issues including the quantitative measurement of parallel evolution in independent lineages and the identification of beneficial mutations.
Article
Twelve populations of Escherichia coli were founded from a single clone and propagated for 2000 generations in identical glucose-limited environments. During this time, the mean fitnesses of the evolving populations relative to their common ancestor improved greatly, but their fitnesses relative to one another diverged only slightly. Although the populations showed similar fitness increases, they may have done so by different underlying adaptations, or they may have diverged in other respects by random genetic drift. Therefore, we examined the relative fitnesses of independently derived genotypes in two other sugars, maltose and lactose, to determine whether they were homogeneous or heterogeneous in these environments. The genetic variation among the derived lines in fitness on maltose and lactose was more than 100-times greater than their variation in fitness on glucose. Moreover, the glucose-adapted genotypes, on average, showed significant adaptation to lactose, but not to maltose. That pathways for use of maltose and glucose are virtually identical in E. coli, except for their distinct mechanisms of uptake, suggests that the derived genotypes have adapted primarily by improved glucose transport. From consideration of the number of generations of divergence, the mutation rate in E. coli, and the proportion of its genome required for growth on maltose (but not glucose), we hypothesize that pleiotropy involving the selected alleles, rather than random genetic drift of alleles at other loci, was the major cause of the variation among the derived genotypes in fitness on these other sugars.
Article
Six replicate populations of the bacterium Escherichia coli were propagated for more than 10,000 generations in a defined environment. We sought to quantify the variation among clones within these populations with respect to their relative fitness, and to evaluate the roles of three distinct population genetic processes in maintaining this variation. On average, a pair of clones from the same population differed from one another in their relative fitness by approximately 4%. This within-population variation was small compared with the average fitness gain relative to the common ancestor, but it was statistically significant. According to one hypothesis, the variation in fitness is transient and reflects the ongoing substitution of beneficial alleles. We used Fisher's fundamental theorem to compare the observed rate of each population's change in mean fitness with the extent of variation for fitness within that population, but we failed to discern any correspondence between these quantities. A second hypothesis supposes that the variation in fitness is maintained by recurrent deleterious mutations that give rise to a mutation-selection balance. To test this hypothesis, we made use of the fact that two of the six replicate populations had evolved mutator phenotypes, which gave them a genomic mutation rate approximately 100-fold higher than that of the other populations. There was a marginally significant correlation between a population's mutation rate and the extent of its within-population variance for fitness, but this correlation was driven by only one population (whereas two of the populations had elevated mutation rates). Under a third hypothesis, this variation is maintained by frequency-dependent selection, whereby genotypes have an advantage when they are rare relative to when they are common. In all six populations, clones were more fit, on average, when they were rare than when they were common, although the magnitude of the advantage when rare was usually small (~1% in five populations and ~5% in the other). These three hypotheses are not mutually exclusive, but frequency-dependent selection appears to be the primary force maintaining the fitness variation within these experimental populations.
Article
We know very little about the genetic basis of adaptation. Indeed, we can make no theoretical predictions, however heuristic, about the distribution of phenotypic effects among factors fixed during adaptation nor about the expected "size" of the largest factor fixed. Study of this problem requires taking into account that populations gradually approach a phenotypic optimum during adaptation via the stepwise substitution of favorable mutations. Using Fisher's geometric model of adaptation, I analyze this approach to the optimum, and derive an approximate solution to the size distribution of factors fixed during adaptation. I further generalize these results to allow the input of any distribution of mutational effects. The distribution of factors fixed during adaptation assumes a pleasingly simple, exponential form. This result is remarkably insensitive to changes in the fitness function and in the distribution of mutational effects. An exponential trend among factors fixed appears to be a general property of adaptation toward a fixed optimum.
Article
We believe that punctuational change dominates the history of life: evolution is concentrated in very rapid events of speciation (geologically instantaneous, even if tolerably continuous in ecological time). Most species, during their geological history, either do not change in any appreciable way, or else they fluctuate mildly in morphology, with no apparent direction. Phyletic gradualism is very rare and too slow, in any case, to produce the major events of evolution. Evolutionary trends are not the product of slow, directional transformation within lineages; they represent the differential success of certain species within a clade—speciation may be random with respect to the direction of a trend (Wright's rule). As an a priori bias, phyletic gradualism has precluded any fair assessment of evolutionary tempos and modes. It could not be refuted by empirical catalogues constructed in its light because it excluded contrary information as the artificial result of an imperfect fossil record. With the model of punctuated equilibria, an unbiased distribution of evolutionary tempos can be established by treating stasis as data and by recording the pattern of change for all species in an assemblage. This distribution of tempos can lead to strong inferences about modes. If, as we predict, the punctuational tempo is prevalent, then speciation—not phyletic evolution—must be the dominant mode of evolution. We argue that virtually none of the examples brought forward to refute our model can stand as support for phyletic gradualism; many are so weak and ambiguous that they only reflect the persistent bias for gradualism still deeply embedded in paleontological thought. Of the few stronger cases, we concentrate on Gingerich's data for Hyopsodus and argue that it provides an excellent example of species selection under our model. We then review the data of several studies that have supported our model since we published it five years ago. The record of human evolution seems to provide a particularly good example: no gradualism has been detected within any hominid taxon, and many are long-ranging; the trend to larger brains arises from differential success of essentially static taxa. The data of molecular genetics support our assumption that large genetic changes often accompany the process of speciation. Phyletic gradualism was an a priori assertion from the start—it was never “seen” in the rocks; it expressed the cultural and political biases of 19th century liberalism. Huxley advised Darwin to eschew it as an “unnecessary difficulty.” We think that it has now become an empirical fallacy. A punctuational view of change may have wide validity at all levels of evolutionary processes. At the very least, it deserves consideration as an alternate way of interpreting the history of life.
Article
Twelve populations of Escherichia coli were founded from a single clone and propagated for 2000 generations in identical glucose-limited environments. During this time, the mean fitnesses of the evolving populations relative to their common ancestor improved greatly, but their fitnesses relative to one another diverged only slightly. Although the populations showed similar fitness increases, they may have done so by different underlying adaptations, or they may have diverged in other respects by random genetic drift. Therefore, we examined the relative fitnesses of independently derived genotypes in two other sugars, maltose and lactose, to determine whether they were homogeneous or heterogeneous in these environments. The genetic variation among the derived lines in fitness on maltose and lactose was more than 100-times greater than their variation in fitness on glucose. Moreover, the glucose-adapted genotypes, on average, showed significant adaptation to lactose, but not to maltose. That pathways for use of maltose and glucose are virtually identical in E. coli, except for their distinct mechanisms of uptake, suggests that the derived genotypes have adapted primarily by improved glucose transport. From consideration of the number of generations of divergence, the mutation rate in E. coli, and the proportion of its genome required for growth on maltose (but not glucose), we hypothesize that pleiotropy involving the selected alleles, rather than random genetic drift of alleles at other loci, was the major cause of the variation among the derived genotypes in fitness on these other sugars.
Article
Previous studies (Gibson et al., 1970; Nestmann and Hill, 1973, Cox and Gibson, 1974) have shown that strains of E. coli with high mutation rates have a marked advantage in competition with wild-type strains. Those studies, however, failed to discriminate between the hypotheses that the mutator bacteria acquired an advantage by evolving faster, on the one hand, or that they had an intrinsic competitive advantage, on the other Our present investigation supports the first hypothesis. We also present estimates for the mutational load in E. coli mutT strains and the mutation rate to higher fitness mutants in these experiments.
Article
Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief.
Article
We know very little about the genetic basis of adaptation. Indeed, we can make no theoretical predictions, however heuristic, about the distribution of phenotypic effects among factors fixed during adaptation nor about the expected 'size' of the largest factor fixed. Study of this problem requires taking into account that populations gradually approach a phenotypic optimum during adaptation via the stepwise substitution of favorable mutations. Using Fisher's geometric model of adaptation, I analyze this approach to the optimum, and derive an approximate solution to the size distribution of factors fixed during adaptation. I further generalize these results to allow the input of any distribution of mutational effects. The distribution of factors fixed during adaptation assumes a pleasingly simple, exponential form. This result is remarkably insensitive to changes in the fitness function and in the distribution of mutational effects. An exponential trend among factors fixed appears to be a general property of adaptation toward a fixed optimum.
Article
New factors arise in a species by the process of mutation. The frequency of mutation is generally small, but it seems probable that it can sometimes be increased by changes in the environment (1,2). On the whole mutants recessive to the normal type occur more commonly than dominants. The frequency of a given type of mutation varies, but for some factors in Drosophila it must be less than 10−6, and is much less in some human cases. We shall first consider initial conditions, when only a few of the new type exist as the result of a single mutation; and then the course of events in a population where the new factor is present in such numbers as to be in no danger of extinction by mere bad luck. In the first section the treatment of Fisher (3) is followed.(Received May 21 1927)(Revised July 25 1927)
Article
Six replicate populations of the bacterium Escherichia coli were propagated for more than 10,000 generations in a defined environment. We sought to quantify the variation among clones within these populations with respect to their relative fitness, and to evaluate the roles of three distinct population genetic processes in maintaining this variation. On average, a pair of clones from the same population differed from one another in their relative fitness by approximately 4%. This within-population variation was small compared with the average fitness gain relative to the common ancestor, but it was statistically significant. According to one hypothesis, the variation in fitness is transient and reflects the ongoing substitution of beneficial alleles. We used Fisher's fundamental theorem to compare the observed rate of each population's change in mean fitness with the extent of variation for fitness within that population, but we failed to discern any correspondence between these quantities. A second hypothesis supposes that the variation in fitness is maintained by recurrent deleterious mutations that give rise to a mutation-selection balance. To test this hypothesis, we made use of the fact that two of the sh replicate populations had evolved mutator phenotypes, which gave them a genomic mutation rate approximately 100-fold higher than that of the other populations. There was a marginally significant correlation between a population's mutation rate and the extent of its within-population variance for fitness, but this correlation was driven by only one population (whereas two of the populations had elevated mutation rates). Under a third hypothesis, this variation is maintained by frequency-dependent selection, whereby genotypes have an advantage when they are rare relative to when they are common. in all six populations, clones were more fit, on average, when they were rare than when they were common, although the magnitude of the advantage when rare was usually small ( similar to 1% in five populations and similar to 5% in the other). These three hypotheses are not mutually exclusive, but frequency-dependent selection appears to be the primary force maintaining the fitness variation within these experimental populations.
Article
This study builds upon an earlier experiment that examined the dynamics of mean fitness in evolving populations of Escherichia coli in which mutations were the sole source of genetic variation. During thousands of generations in a constant environment, the rate of improvement in mean fitness of these asexual populations slowed considerably from an initially rapid pace. In this study, we sought to determine whether sexual recombination with novel genotypes would reaccelerate the rate of adaption in these populations. To that end, treatment populations were propagated for an additional 1000 generations in the same environment as their ancestors, but they were periodically allowed to mate with an immigrant pool of genetically distinct Hfr (high frequency recombination) donors. These donors could transfer genes to the resident populations by conjugation, but the donors themselves could not grow in the experimental environment. Control populations were propagated under identical conditions, but in the absence of sexual recombination with the donors. All twelve control populations retained the ancestral alleles at every locus that was scored. In contrast, the sexual recombination treatment yielded dramatic increases in genetic variation. Thus, there was a profound effect of recombination on the rate of genetic change. However, the increased genetic variation in the treatment populations had no significant effect on the rate of adaptive evolution, as measured by changes in mean fitness relative to a common competitor. We then considered three hypotheses that might reconcile these two outcomes: recombination pressure, hitchhiking of recombinant genotypes in association with beneficial mutations, and complex selection dynamics whereby certain genotypes may have a selective advantage only within a particular milieu of competitors. The estimated recombination rate was too low to explain the observed rate of genetic change, either alone or in combination with hitchhiking effects. However, we documented comple x ecological interactions among some recombinant genotypes, suggesting that our method for estimating fitness relative to a common competitor might have underestimated the rate of adaptive evolution in the treatment populations.
Article
... Stephen Jay Gould and Niles Eldredge Abstract.-We believe that punctuational change dominates the history of life: evolution is concentrated in very rapid events of speciation (geologically instantaneous, even if tolerably continuous in ecological time). ... Stephen Jay Gould . ...
Article
We assess the degree to which adaptation to a uniform environment among independently evolving asexual populations is associated with increasing divergence of those populations. In addition, we are concerned with the pattern of adaptation itself, particularly whether the rate of increase in mean fitness tends to decline with the number of generations of selection in a constant environment. The correspondence between the rate of increase in mean fitness and the within-population genetic variance of fitness, as expected from Fisher's fundamental theorem, is also addressed. Twelve Escherichia coli populations were founded from a single clonal ancestor and allowed to evolve for 2,000 generations. Mean fitness increased by about 37%. However, the rate of increase in mean fitness was slower in later generations. There was no statistically significant within-population genetic variance of fitness, but there was significant between-population variance. Although the estimated genetic variation in fitness within populations was not statistically significant, it was consistent in magnitude with theoretical expectations. Similarly, the variance of mean fitness between populations was consistent with a model that incorporated stochastic variation in the timing and order of substitutions at a finite number of nonepistatic loci, coupled with substitutions delays and interference between substitutions arising from clonality. These results, taken as a whole, are consistent with theoretical expectations that do not invoke divergence due to multiple fitness peaks in a Wrightian evolutionary landscape.
Article
Rates of spontaneous mutation per genome as measured in the laboratory are remarkably similar within broad groups of organisms but differ strikingly among groups. Mutation rates in RNA viruses, whose genomes contain ca. 10(4) bases, are roughly 1 per genome per replication for lytic viruses and roughly 0.1 per genome per replication for retroviruses and a retrotransposon. Mutation rates in microbes with DNA-based chromosomes are close to 1/300 per genome per replication; in this group, therefore, rates per base pair vary inversely and hugely as genome sizes vary from 6 x 10(3) to 4 x 10(7) bases or base pairs. Mutation rates in higher eukaryotes are roughly 0.1-100 per genome per sexual generation but are currently indistinguishable from 1/300 per cell division per effective genome (which excludes the fraction of the genome in which most mutations are neutral). It is now possible to specify some of the evolutionary forces that shape these diverse mutation rates.
Article
Natural selection can adjust the rate of mutation in a population by acting on allelic variation affecting processes of DNA replication and repair. Because mutation is the ultimate source of the genetic variation required for adaptation, it can be appealing to suppose that the genomic mutation rate is adjusted to a level that best promotes adaptation. Most mutations with phenotypic effects are harmful, however, and thus there is relentless selection within populations for lower genomic mutation rates. Selection on beneficial mutations can counter this effect by favoring alleles that raise the mutation rate, but the effect of beneficial mutations on the genomic mutation rate is extremely sensitive to recombination and is unlikely to be important in sexual populations. In contrast, high genomic mutation rates can evolve in asexual populations under the influence of beneficial mutations, but this phenomenon is probably of limited adaptive significance and represents, at best, a temporary reprieve from the continual selection pressure to reduce mutation. The physiological cost of reducing mutation below the low level observed in most populations may be the most important factor in setting the genomic mutation rate in sexual and asexual systems, regardless of the benefits of mutation in producing new adaptive variation. Maintenance of mutation rates higher than the minimum set by this "cost of fidelity" is likely only under special circumstances.
Article
We studied the evolution of high mutation rates and the evolution of fitness in three experimental populations of Escherichia coli adapting to a glucose-limited environment. We identified the mutations responsible for the high mutation rates and show that their rate of substitution in all three populations was too rapid to be accounted for simply by genetic drift. In two of the populations, large gains in fitness relative to the ancestor occurred as the mutator alleles rose to fixation, strongly supporting the conclusion that mutator alleles fixed by hitchhiking with beneficial mutations at other loci. In one population, no significant gain in fitness relative to the ancestor occurred in the population as a whole while the mutator allele rose to fixation, but a substantial and significant gain in fitness occurred in the mutator subpopulation as the mutator neared fixation. The spread of the mutator allele from rarity to fixation took >1000 generations in each population. We show that simultaneous adaptive gains in both the mutator and wild-type subpopulations (clonal interference) retarded the mutator fixation in at least one of the populations. We found little evidence that the evolution of high mutation rates accelerated adaptation in these populations.
Article
It is generally accepted from the darwinian theory of evolution that a progressive increase in population adaptation will occur in populations containing genetic variation in fitness, until a stable equilibrium is reached and/or the additive genetic variation is exhausted. However, the theoretical literature of population genetics documents exceptions where mean population fitness may decrease in response to evolutionary changes in gene frequency, due to varying selective coefficients, sexual selection or to epistatic interactions between loci. Until now, no examples of such exceptions have been documented from fitness estimates in either natural or experimental populations. We present here direct evidence that, as a result of epistatic interactions between adaptive mutations, mean population fitness can decrease in asexual evolving populations of the yeast Saccharomyces cerevisiae.
Evolution of high mutation rates in experimental populations of Escherichia coli
  • Sniegowski