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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
- 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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