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Title
Host-symbiont coevolution in digital and microbial systems
Creator
Zaman, Luis
Date
2014
Collection
Electronic Theses & Dissertations
Description
Darwin's image of the entangled bank captures foremost the pervasiveness of life as it clothes the earth, but it also captures how intimately species interact and often depend on one another. This interaction is particularly pronounced for obligate parasites, who's livelihoods depend on interactions with their hosts and who's hosts often pay severely. In my thesis, I first demonstrate how antagonistic coevolution in Avida leads to a diverse set of interacting host and parasite phenotypes: a...
Show moreDarwin's image of the entangled bank captures foremost the pervasiveness of life as it clothes the earth, but it also captures how intimately species interact and often depend on one another. This interaction is particularly pronounced for obligate parasites, who's livelihoods depend on interactions with their hosts and who's hosts often pay severely. In my thesis, I first demonstrate how antagonistic coevolution in Avida leads to a diverse set of interacting host and parasite phenotypes: a digital entangled bank. Second, I show how further evolution is embedded within this community context by studying the coevolution of complexity driven by parasites'population genetic memory -- where the diversifying community of parasites "remembers" previously evolved hosts. Continuing to study the intersection of coevolution and community ecology, I investigate the structure of communities produced by the coevolutionary process in Avida. I show that a nested structure of interactions is common in our experiments, which is the same structure often found in natural host-parasite and plant-pollinator communities as well as many phage-bacteria interaction networks. In addition, I show that "growing" networks are nested by virtue of the process of incrementally adding nodes and edges. Thus, coevolution is expected to produce significantly nested communities when compared to random networks. However, the coevolved digital host-parasite networks are significantly more nested than expected from this neutral growth process. The interactions between hosts and their intimately interacting partners are not just parasitic, instead they span a broad range and include many mutualistic interactions. In the last section of my thesis, I study evolution and coevolution along the parasitism-mutualism continuum using a temperate λ phage system that provides its host with access to an otherwise unavailable metabolic pathway. Instead of evolving more mutualistic phage as I predicted, both the phage and bacteria evolved cheating strategies.
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Title
Deconstructing the correlated nature of ancient and emergent traits : an evolutionary investigation of metabolism, morphology, and mortality
Creator
Grant, Nkrumah Alions
Date
2020
Collection
Electronic Theses & Dissertations
Description
Phenotypic correlations are products of genetic and environmental interactions, yet the nature of these correlations is obscured by the multitude of genes organisms possess. My dissertation work focused on using 12 populations of Escherichia coli from Richard Lenski's long-term evolution experiment (LTEE) to understand how genetic correlations facilitate or impede an organism's evolution. In chapter 1, I describe how ancient correlations between aerobic and anaerobic metabolism have...
Show morePhenotypic correlations are products of genetic and environmental interactions, yet the nature of these correlations is obscured by the multitude of genes organisms possess. My dissertation work focused on using 12 populations of Escherichia coli from Richard Lenski's long-term evolution experiment (LTEE) to understand how genetic correlations facilitate or impede an organism's evolution. In chapter 1, I describe how ancient correlations between aerobic and anaerobic metabolism have maintained - and even improved - the capacity of E. coli to grow in an anoxic environment despite 50,000 generations of relaxed selection for anaerobic growth. I present genomic evidence illustrating substantially more mutations have accumulated in anaerobic-specific genes and show parallel evolution at two genetic loci whose protein products regulate the aerobic-to-anaerobic metabolic switch. My findings reject the "if you don't use it, you lose it" notion underpinning relaxed selection and show modules with deep evolutionary roots can overlap more, hence making them harder to break. In chapter 2, I revisit previous work in the LTEE showing that the fitness increases measured for the 12 populations positively correlated with an increase in cell size. This finding was contrary to theory predicting smaller cells should have evolved. Sixty thousand generations have surpassed since that initial study, and new fitness data collected for the 12 populations show fitness has continued to increase over this period. Here, I asked whether cell size also continued to increase. To this end, I measured the size of cells for each of the 12 populations spanning 50,000 generations of evolution using a particle counter, microscopy, and machine learning. I show cell size has continued to increase and that it remains positively correlated with fitness. I also present several other observations including heterogeneity in cell shape and size, parallel mutations in cell-shape determining genes, and elevated cell death in the single LTEE population that evolved a novel metabolism - namely the ability to grow aerobically on citrate. This last observation formed the basis of my chapter 3 research where my collaborators and I fully examine the cell death finding and the associated genotypic and phenotypic consequences of the citrate metabolic innovation.
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Title
The effects of genetic background on the evolution of antibiotic resistance and its fitness costs
Creator
Card, Kyle Joseph
Date
2020
Collection
Electronic Theses & Dissertations
Description
Antibiotic resistance is a growing public-health concern. Efforts to control the emergence and spread of resistance would benefit from an improved ability to forecast when and how it will evolve. To predict the evolution of resistance with accuracy, we must understand and integrate information about many factors, including a bacterium's evolutionary history. This dissertation centers on the effects of genetic background on the evolution of phenotypic resistance, its genetic basis, and its...
Show moreAntibiotic resistance is a growing public-health concern. Efforts to control the emergence and spread of resistance would benefit from an improved ability to forecast when and how it will evolve. To predict the evolution of resistance with accuracy, we must understand and integrate information about many factors, including a bacterium's evolutionary history. This dissertation centers on the effects of genetic background on the evolution of phenotypic resistance, its genetic basis, and its fitness costs. To address these issues, I used Escherichia coli strains from the long-term evolution experiment (LTEE) that independently evolved for multiple decades in an environment without antibiotics.First, I examined how readily these LTEE strains could overcome prior losses of intrinsic resistance through subsequent evolution when challenged with antibiotics. Second, I investigated whether lineages founded from different genotypes take parallel or divergent mutational paths to achieve increased resistance. Third, I tested whether fitness costs of resistance mutations are constant across different genetic backgrounds. In these studies, I focused attention on the interplay between repeatability and contingency in the evolutionary process. My findings demonstrate that genetic background can influence both the phenotypic and genotypic evolution of resistance and its associated fitness costs. I conclude this dissertation with a broader discussion about these and other factors that can influence the evolution of antibiotic resistance, and their clinical and public-health implications.
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Title
Coevolution of bacterial-phage interactions
Creator
Meyer, Justin R.
Date
2012
Collection
Electronic Theses & Dissertations
Description
Bacteria and their viruses, phage, are the most abundant and genetically diverse group of organisms on earth. Given their prevalence, it is no wonder that recent studies have found their interactions important for ecosystem function, as well as the health of humans. Unfortunately, because of technical challenges with studying microbes, some of the most basic questions on their interactions, such as who infects whom, and how their relationships evolved in the first place, remain unanswered....
Show moreBacteria and their viruses, phage, are the most abundant and genetically diverse group of organisms on earth. Given their prevalence, it is no wonder that recent studies have found their interactions important for ecosystem function, as well as the health of humans. Unfortunately, because of technical challenges with studying microbes, some of the most basic questions on their interactions, such as who infects whom, and how their relationships evolved in the first place, remain unanswered. Here I report six studies on bacterial-phage interactions, each focused on understanding their pattern and the underlying biophysical, ecological, and evolutionary processes that shape them. To do this, I tested a number of hypotheses using laboratory experiments and analyses of natural microbial diversity. First, I tested whether Esherichia coli cultured without phage would counter-intuitively evolve new interactions with phage. Typically bacterial traits responsible for phage resistance have pleiotropic consequences on growth, therefore as a side-effect of adapting to an abiotic environment, bacteria may also evolve to become more or less vulnerable to their parasites. After 45,000 generations of laboratory culturing without phage, E. coli gained resistance to lambda phage, gained sensitivity to a mutant T6 phage, and remained resistant to wild type T6. Each response was explained by understanding the pleiotropic costs or benefits of mutations that confer resistance. Because of pleiotropy, interactions may even evolve in the absence of one player.For the rest of my studies I examined how interactions evolve when host and parasite co-occur. First, I found that when E. coli and phage lambda are cocultured, E. coli evolves resistance by reducing the number of phage genotypes that can infect it, whereas, lambda evolves to increase the number of bacterial genotypes it can infect. This antagonism produces a interaction matrix with a nested form where less derived host-ranges fall one within another. To determine whether this nested pattern is an artifact of the labratory environment, or if the pattern is general to natural communities, I performed a metaanalysis on already published phage-bacterial interaction matrices. The majority of networks were significantly nested (28 of 38). Lastly, I examined the molecular basis of E. coli resistance to lambda and found that resistance often evolves through mutations in E. coli's lamB, the gene for the phage receptor. Also, the strength of resistance is correlated with how the mutation perturbs the orientation specific features of the protein structure, primarily loop four which extends out of the cell membrane. For the final two chapters, I studied whether lambda could evolve to target a novel receptor and the evolutionary consequences of such an innovation. Under particular laboratory conditions, E. coli evolves resistance by down-regulating LamB, which sets the stage for lambda to evolve the necessary mutations to exploit a new protein receptor. When allowed to coevolve under this condition, lambda evolved to exploit another outer-membrane protein, OmpF. This new function is the result of a particular combination of four mutations in J, the gene for the protein ligand lambda uses to bind to its host. Once lambda evolves this novel interaction, an evolutionary arms-race begins that drives rapid diversification of the bacteria and phage. Overall, my studies show that coevolution between bacteria and phage, whether it be in the lab or in nature, produces nested interactions matrices. Secondly, antagonistic coevolution is a creative process able to generate new genotypes of host and parasite and promote the evolution of novel function. Lastly, costs for resistance have many important effects, from determining whether resistance will evolve or be lost, to the generation of diversity.
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Title
Replaying Life's Virtual Tape : Examining the Role of History in Experiments with Digital Organisms
Creator
Bundy, Jason Nyerere
Date
2021
Collection
Electronic Theses & Dissertations
Description
Evolution is a complex process with a simple recipe. Evolutionary change involves three essential “ingredients” interacting over many generations: adaptation (selection), chance (random variation), and history (inheritance). In 1989’s Wonderful Life, the late paleontologist Stephen Jay Gould advocated for the importance of historical contingency—the way unique events throughout history influence future possibilities—using a clever thought experiment of “replaying life’s tape”. But not...
Show moreEvolution is a complex process with a simple recipe. Evolutionary change involves three essential “ingredients” interacting over many generations: adaptation (selection), chance (random variation), and history (inheritance). In 1989’s Wonderful Life, the late paleontologist Stephen Jay Gould advocated for the importance of historical contingency—the way unique events throughout history influence future possibilities—using a clever thought experiment of “replaying life’s tape”. But not everyone was convinced. Some believed that chance was the primary driver of evolutionary change, while others insisted that natural selection was the most powerful influence. Since then, “replaying life’s tape” has become a core method in experimental evolution for measuring the relative contributions of adaptation, chance, and history. In this dissertation, I focus on the effects associated with history in evolving populations of digital organisms—computer programs that self-replicate, mutate, compete, and evolve in virtual environments. In Chapter 1, I discuss the philosophical significance of Gould’s thought experiment and its influence on experimental methods. I argue that his thought experiment was a challenge to anthropocentric reasoning about natural history that is still popular, particularly outside of the scientific community. In this regard, it was his way of advocating for a “radical” view of evolution. In Chapter 2—Richard Lenski, Charles Ofria, and I describe a two-phase, virtual, “long-term” evolution experiment with digital organisms using the Avida software. In Phase I, we evolved 10 replicate populations, in parallel, from a single genotype for around 65,000 generations. This part of the experiment is similar to the design of Lenski’s E. coli Long-term Evolution Experiment (LTEE). We isolated the dominant genotype from each population around 3,000 generations (shallow history) into Phase I and then again at the end of Phase I (deep history). In Phase II, we evolved 10 populations from each of the genotypes we isolated from Phase I in two new environments, one similar and one dissimilar to the old environment used for Phase I. Following Phase II, we estimated the contributions of adaptation, chance, and history to the evolution of fitness and genome length in each new environment. This unique experimental design allowed us to see how the contributions of adaptation, chance, and history changed as we extended the depth of history from Phase I. We were also able to determine whether the results depended on the extent of environmental change (similar or dissimilar new environment). In Chapter 3, we report an extended analysis of the experiment from the previous chapter to further examine how extensive adaptation to the Phase I environment shaped the evolution of replicates during Phase II. We show how the form of pleiotropy (antagonistic or synergistic) between the old (Phase I) and new (Phase II) habitats was influenced by the depth of history from Phase I (shallow or deep) and the extent of environmental change (similar or dissimilar new environment). In the final chapter Zachary Blount, Richard Lenski, and I describe an exercise we developed using the educational version of Avida (Avida-ED). The exercise features a two-phase, “replaying life’s tape” activity. Students are able to explore how the unique history of founders that we pre-evolved during Phase I influences the acquisition of new functions by descendent populations during Phase II, which the students perform during the activity.
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Title
Coevolutionary implications of envelope-mediated resistance to phage
Creator
Burmeister, Alita
Date
2017
Collection
Electronic Theses & Dissertations
Description
This dissertation concerns the coevolution of pathogens and their hosts. For my thesis, I have worked with Escherichia coli and phage using experimental evolution, molecular biology, and theory that describes general host-pathogen interactions. This work centers on three themes of broad interest to evolutionary biology and microbiology: coevolutionary origins of novelty and diversity, the role of tradeoffs in constraining evolvability, and the ecological impacts of host resistance.In Chapter...
Show moreThis dissertation concerns the coevolution of pathogens and their hosts. For my thesis, I have worked with Escherichia coli and phage using experimental evolution, molecular biology, and theory that describes general host-pathogen interactions. This work centers on three themes of broad interest to evolutionary biology and microbiology: coevolutionary origins of novelty and diversity, the role of tradeoffs in constraining evolvability, and the ecological impacts of host resistance.In Chapter 1, I worked with a set of experimentally coevolved E. coli/ communities to investigate the bacterial genes that gained mutations and whether fitness tradeoffs had constrained the evolution of those mutations. To do this, I isolated bacteria from the coevolution experiment and sequenced the genomes of the isolates. I found resistance mutations that modified the expression or sequence of proteins used by during infection: LamB and OmpF at the outer membrane, and ManY and ManZ at the inner membrane. To test for fitness tradeoffs, I estimated the isolates’ fitness in the presence and absence of . Phage selection strongly favored resistance mutations, despite those mutations incurring pleiotropic costs related to resource acquisition and homeostasis.For my second chapter, I was particularly interested in the E. coli manY and manZ mutations that allowed phage to adsorb to the outside of the cell but limited the phage’s ability to eject its genome into the cytoplasm. I thought that these mutations might effectively “trap” phage in non-productive infections, thereby accelerating the rate of phage loss from the extracellular environment. However, I found no evidence for such traps; instead, had evolved independence of manY and manZ. These results indicate that for each of the known resistance-conferring mutations evolved by E. coli, the coevolving populations discovered evolutionary routes to circumvent the resistance. For Chapter 3, I shifted briefly from laboratory experiments to mathematical theory to further investigate the trap idea. Although it turned out that the manY and manZ mutations don’t act as traps, I was more generally interested in host defenses on the inside of the cell, such as CRISPR-Cas defense and restriction enzymes, which exist for many bacterial species. Comparable to other studies on parasite traps in animal hosts, I used theory to predict that in the presence of trap alleles, bacteriophage densities would be lower than they otherwise would be, even if more permissive hosts were available to them.In my final chapter, I returned to the coevolution experiment with E. coli and . Although it was known that laboratory populations of phage evolved to use OmpF, and that this function required multiple mutations in the phage J gene, it was unknown how those mutations accumulated. I studied how both phage J gene mutations and bacterial malT (a positive regulator of lamB) mutations influenced the phage’s adaptive landscape. I found that bacterial evolution strongly affected selection patterns on different phage genotypes: in many cases the evolution of host resistance more strongly favored increased phage adsorption rate. Because of that, the evolutionary intermediates between the ancestral and OmpF-infecting phage were positively selected, revealing that host coevolution can increase the rate at which phage evolve to use novel host structures.
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Title
Experimental evolution and ecological consequences : new niches and changing stoichiometry
Creator
Turner, Caroline B.
Date
2015
Collection
Electronic Theses & Dissertations
Description
Evolutionary change can alter the ecological conditions in which organisms live and continue to evolve. My dissertation research used experimental evolution to study two aspects of evolutionary change with ecological consequences: the generation of new ecological niches and evolution of the elemental composition of biomass. I worked with the long-term evolution experiment (LTEE), which is an ongoing experiment in which E. coli have evolved under laboratory conditions for more than 60,000...
Show moreEvolutionary change can alter the ecological conditions in which organisms live and continue to evolve. My dissertation research used experimental evolution to study two aspects of evolutionary change with ecological consequences: the generation of new ecological niches and evolution of the elemental composition of biomass. I worked with the long-term evolution experiment (LTEE), which is an ongoing experiment in which E. coli have evolved under laboratory conditions for more than 60,000 generations. The LTEE began with extremely simple ecological conditions. Twelve populations were founded from a single bacterial genotype and growth was limited by glucose availability. In Chapter 1, I focused on a population within the LTEE in which some of the bacteria evolved the ability to consume a novel resource, citrate. Citrate was present in the growth media throughout the experiment, but E. coli is normally unable to consume it under aerobic conditions. The citrate consumers (Cit+) coexisted with a clade of bacteria which were unable to consume citrate (Cit-). Specialization on glucose, the standard carbon source in the LTEE, was insufficient to explain the frequency-dependent coexistence of Cit- with Cit+. Instead Cit– evolved to cross-feed on molecules released by Cit+. The evolutionary innovation of citrate consumption led to a more complex ecosystem in which two co-existing ecotypes made use of five different carbon sources.After 10,000 generations of coexistence, Cit- went extinct from the population (Chapter 2). I conducted replay experiments, re-evolving for 500 generations 20 replicate populations from prior to extinction. Cit- was retained in all populations, indicating that the extinction was not deterministic. Furthermore, when I added small numbers of Cit- to the population after extinction, Cit- was able to reinvade. It therefore appears that the Cit- extinction was not due to exclusion by Cit+, but rather to unknown laboratory variation.Chapter 3 shifts focus to studying evolutionary changes in stoichiometry, the ratio of different elements within organisms’ biomass. Variation in stoichiometry between organisms has important ecological consequences, but the evolutionary origin of that variation had not previously been studied experimentally. Growth in the LTEE is carbon limited and nitrogen and phosphorus are abundant. Additionally, daily transfer to fresh media selects for increased growth rate, which other research has suggested correlates to higher phosphorus content. Consistent with our predictions based on this environment, clones isolated after 50,000 generations of evolution had significantly higher nitrogen and phosphorus content than ancestral clones. There was no change in the proportion of carbon in biomass, but the total amount of carbon retained in biomass increased, indicating that the bacteria also evolved higher carbon use efficiency.To test whether the increases in nitrogen and phosphorus observed in the LTEE were a result of carbon limitation or were side effects of other selective factors in the experiment, I evolved clones from the LTEE for 1000 generations under nitrogen rather than carbon limitation (Chapter 4). The stoichiometry of the bacteria did change over the course of 1000 generations, indicating that evolution of stoichiometry can occur over relatively short time frames. Unexpectedly however, the evolved bacteria had higher nitrogen and phosphorus content. It appears that the bacteria were initially poor at incorporating nitrogen into biomass, but evolved improved nitrogen uptake.
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Title
Evolution of laboratory and natural populations of Escherichia coli
Creator
Maddamsetti, Rohan
Date
2016
Collection
Electronic Theses & Dissertations
Description
My dissertation spans two dichotomies: evolution in the laboratory versus evolution in nature, and asexual versus sexual evolutionary dynamics. In Chapter 1 I describe asexual evolutionary dynamics in one population of Lenski’s long-term evolution experiment with Escherichia coli. I describe cohorts of mutations that sweep to fixation together as characteristic of clonal interference dynamics. I also describe an ecological interaction that evolved and then went extinct after thousands of...
Show moreMy dissertation spans two dichotomies: evolution in the laboratory versus evolution in nature, and asexual versus sexual evolutionary dynamics. In Chapter 1 I describe asexual evolutionary dynamics in one population of Lenski’s long-term evolution experiment with Escherichia coli. I describe cohorts of mutations that sweep to fixation together as characteristic of clonal interference dynamics. I also describe an ecological interaction that evolved and then went extinct after thousands of generations, and discuss how such interactions affect cohorts of mutations. In Chapter 2 I report that conserved core genes tend to be targets of selection in the long-term experiment. In Chapter 3, I investigate the surprising observation that synonymous genetic diversity is not uniform across the genomes of natural E. coli isolates. This observation is surprising because in clonal organisms with a constant point mutation rate, synonymous diversity should be constant across the genome. I use patterns of synonymous mutations in the long-term experiment to argue that genome-wide variation in the mutation rate does not adequately explain patterns of synonymous genetic diversity. In Chapter 4, I propose that recombination and gene flow could account for genome-wide variation in synonymous genetic diversity. In Chapter 5, I analyze E. coli genomes isolated from an evolution experiment with recombination in which E. coli K-12 with known growth defects could donate genetic material to recipient populations founded by long-term experiment clones. The degree of recombination varied dramatically across sequenced clones. The strongest predictor of successful transfer was proximity to the oriT origin of transfer in the K-12 donors. Donor alleles close to oriT replaced their recipient counterparts at a high rate, and in many of those cases, known beneficial mutations in the recipients were replaced by donor alleles.
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Title
The evolution of a key innovation in an experimental population of Escherichia coli : a tale of opportunity, contingency, and co-option
Creator
Blount, Zachary David
Date
2011
Collection
Electronic Theses & Dissertations
Description
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 ...
Show moreThe 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.
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Title
An analysis of fitness in long-term asexual evolution experiments
Creator
Wiser, Michael J.
Date
2015
Collection
Electronic Theses & Dissertations
Description
Evolution is the central unifying concept of modern biology. Yet it can be hard to study in natural system, as it unfolds across generations. Experimental evolution allows us to ask questions about the process of evolution itself: How repeatable is the evolutionary process? How predictable is it? How general are the results? To address these questions, my collaborators and I carried out experiments both within the Long-Term Evolution Experiment (LTEE) in the bacteria Escherichia coli, and the...
Show moreEvolution is the central unifying concept of modern biology. Yet it can be hard to study in natural system, as it unfolds across generations. Experimental evolution allows us to ask questions about the process of evolution itself: How repeatable is the evolutionary process? How predictable is it? How general are the results? To address these questions, my collaborators and I carried out experiments both within the Long-Term Evolution Experiment (LTEE) in the bacteria Escherichia coli, and the digital evolution software platform Avida. In Chapter 1, I focused on methods. Previous research in the LTEE has relied on one particular way of measuring fitness, which we know becomes less precise as fitness differentials increase. I therefore decided to test whether two alternate ways of measuring fitness would improve precision, using one focal population. I found that all three methods yielded similar results in both fitness and coefficient of variation, and thus we should retain the traditional method.In Chapter 2, I turned to measuring fitness in each of the populations. Previous work had considered fitness to change as a hyperbola. A hyperbolic function is bounded, and predicts that fitness will asymptotically approach a defined upper bound; however, we knew that fitness in these populations routinely exceeded the asymptotic limit calculated from a hyperbola fit to the earlier data. I instead used to a power law, a mathematical function that does not have an upper bound. I found that this function substantially better describes fitness in this system, both among the whole set of populations, and in most of the individual populations. I also found that the power law models fit on just early subsets of the data accurately predict fitness far into the future. This implies that populations, even after 50,000 generations of evolution in consistent environment, are so far from the tops of fitness peaks that we cannot detect evidence of those peaks.In Chapter 3, I examined to how variance in fitness changes over long time scales. The among-population variance over time provides us information about the adaptive landscape on which the populations have been evolving. I found that among-population variance remains significant. Further, competitions between evolved pairs of populations reveal additional details about fitness trajectories than can be seen from competitions against the ancestor. These results demonstrate that our populations have been evolving on a complex adaptive landscape.In Chapter 4, I examined whether the patterns found in Chapter 2 apply to a very different evolutionary system, Avida. This system incorporates many similar evolutionary pressures as the LTEE, but without the details of cellular biology that underlie nearly all organic life. I find that in both the most complex and simplest environments in Avida, fitness also follows the same power law dynamics as seen in the LTEE. This implies that power law dynamics may be a general feature of evolving systems, and not dependent on the specific details of the system being studied.
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