Michigan State University

MSU Libraries

Digital Repository

Search results

(1 - 3 of 3)
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.
Show less
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.
Show less
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.
Show less