Browsing by Subject "evolution"

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Breaking the weakest link: Evolution and ecology of antibiotic tolerance in cross-feeding bacterial communities
(2019-05) Adamowicz, Elizabeth
Microbes frequently rely on metabolites excreted by other bacterial species, but little is known about how this cross-feeding influences the effect of antibiotics. We hypothesized that when species rely on each other for essential metabolites, the minimum inhibitory concentration (MIC) for all species will drop to that of the "weakest link"— the species least resistant in monoculture. We tested this hypothesis in an obligate cross-feeding system that was engineered between Escherichia coli, Salmonella enterica, and Methylobacterium extorquens. The effect of tetracycline and ampicillin were tested on both liquid and solid media. In all cases, resistant species were inhibited at significantly lower antibiotic concentrations in the cross-feeding community than in monoculture or a competitive community. However, deviation from the "weakest link" hypothesis was also observed in cross-feeding communities apparently as a result of changes in the timing of growth and cross-protection. Comparable results were also observed in a clinically relevant system involving facultative cross-feeding between Pseudomonas aeruginosa and an anaerobic consortium found in the lungs of cystic fibrosis patients. P. aeruginosa was inhibited by lower concentrations of ampicillin when cross-feeding than when grown in isolation. These results suggest that cross-feeding significantly alters tolerance to antibiotics in a variety of systems.
Darwin and the Digital Body: Evolution, Posthumanism, and Imaginative Spaces of Possibility
(2012-05-30) Fierke, Jennifer
Talking about embodiment is political, whether the discussion is about “race,” gender, “ability,” size or body modification. Despite significant leaps forward in equity during the twentieth century, beings continue to be constrained—practically, intellectually, emotionally, sexually, and expressively—because of how we imagine bodies. This project brings embodiment into relief by focusing on two seemingly disparate theories: Victorian evolutionary theory and posthumanism. Both are explored via the dual lenses of nineteenth-century speculative fiction and works of fantastic digital media, providing theoretical and cultural frameworks for challenging dominant paradigms of embodiment.
Darwin, Huxley, and the Nineteenth-Century Rhetoric of Science
(2016-09) Wright, Jeffrey
The interactions between Charles Darwin and Thomas Henry Huxley are widely misunderstood. Huxley neither rejected Darwin’s core ideas nor accepted them uncritically; instead, each scientist strongly influenced the other over a period of several decades. Fully understanding their debate requires understanding the rhetoric of the time, which leads to a realization that nineteenth-century scientists were familiar with a rhetoric of science that addresses many of the same issues that the discipline does today. The rhetorician Benjamin Humphrey Smart, although almost forgotten today, was highly influential not only on Darwin, but on the physicist Michael Faraday and the philosopher of science John Stuart Mill. His ideas set much of the background for the debate.
Discovering Ecological and Evolutionary Principles Governing Microbial Community Responses to Bacteriophage Infection of a Cross-Feeding Synthetic Coculture and Implications for Phage-based Applications
(2020-08) Fazzino, Lisa
Bacterial viruses, called bacteriophage (phage), infect bacteria and alter microbial community structure. Phages are an untapped resource to manipulate agriculture and medically applicable microbial communities. Yet, we cannot predict how phage impact a microbial community. My research aims to uncover ecological and evolutionary principles governing responses of microbial communities that contain cross-feeding interactions, where one species provides nutrients to (‘feeds’) another, phage. I combine wet-lab experiments on an engineered microbial co-culture with mathematical modeling to explore aspects of phage infection that are difficult to manipulate experimentally. I use a cross-feeding bacterial co-culture with Escherichia coli (E. coli) and Salmonella enterica (S. enterica) bacterial strains. In this cross-feeding system, E. coli cannot produce methionine, but does produce acetate and galactose. E. coli is paired with S. enterica that over-produces methionine and consumes acetate and galactose that E. coli secretes. To this co-culture, I add phage that infect either species. I have asked how simple cross-feeding co-cultures respond to phage infection. In Chapter 2, I used mathematical modeling and wet-lab experiments to show that single phage infections can break the cross-feeding relationship by liberating nutrients previously sequestered in the infected bacterial cells, ultimately changing community composition, and that partial, not full, resistance was necessary for this effect. In Chapter 3, ‘cocktails’ made of two different phage suppressed community growth the longest in a novel formulation that targeted both the pathogenic bacterial species and the slowest growing cross-feeder. Mathematical modeling showed that this was a generalizable concept to all cross-feeding systems. In Chapter 4, despite impacting community structure, I found that long term co-evolution between phage and E. coli cross-feeding with S. enterica only had weak effects on rates of adaptation. Phage treatments tended to increase rates of adaptations, as predicted by the Red Queen hypothesis, and cross-feeding tended to decrease rates of adaptation, as predicted by the Red King hypothesis. Overall, this thesis helps set baseline expectations of how phage influence cross-feeding microbial communities.
Emergence and Stability of Self-Evolved Cooperative Strategies using Stochastic Machines
(2019-12) Kuan, Jin H; Salecha, Aadesh
To investigate the origin of cooperative behaviors, we developed an evolutionary model of sequential strategies and tested our model with computer simulations. The sequential strategies represented by stochastic machines were evaluated through games of iterated Prisoner's Dilemma (PD) with other agents in the population, allowing bootstrapping evolution to occur. We expanded upon past works by proposing a novel mechanism to mutate stochastic Moore machines that introduces a greater spectrum of evolvable machines. These machines were then subjected to various selection mechanisms and the resulting evolved strategies were analyzed. We found that cooperation can indeed emerge spontaneously in evolving populations playing iterated PD, specifically in the form of trigger strategy. In addition, the strategy was found to be resilient towards mutation and thus is evolutionarily stable. To verify the validity of the proposed mutation mechanism, we also evolved the machines to play other 2x2 games such as Chicken and Stag's Hunt, and obtained interesting strategies that demonstrate a degree of Pareto optimality.
Estimating the capacity of Chamaecrista fasciculata to adapt to novel environments
(2021-12) Peschel, Anna
Tallgrass prairies are one of the most endangered ecosystems in North America with less than 1 percent of their original extent prior to European settlement remaining. Most tallgrass prairie has been razed for agriculture because they tend to exist on fertile soils. In Minnesota the tallgrass prairie once covered 18 million acres, but now only 200,000 acres remain—small, fragmented patches in a matrix of corn and soybean fields (Minnesota Prairie Plan Working Group 2018).Climate change poses new management challenges for extant tallgrass prairies. Given that the remaining prairies are small and severed from gene flow, they may lack sufficient genetic variation to adapt to climate change. If the standing genetic diversity within a population is insufficient for adaptive evolution, seed may need to be sourced from other populations to introduce alleles adaptive in environments predicted for the future. However, how tallgrass prairie plant populations will respond to climate change, and if they possess the capacity to adapt to climate change in situ, are open questions. With insight from prior research (Etterson 2004a,b; Sheth et al. 2018; Kulbaba et al. 2019), we investigate the capacity of the annual prairie legume, Chamaecrista fasciculata, to adapt to environments predicted for the future. The overarching aims of this research are to 1) estimate adaptive capacity in a population of C. fasciculata, 2) test fundamental evolutionary theory predicting a populations’ rate of adaptation, and 3) identify how key plant traits may respond to, and modulate a population’s response to, future climate change. Along with increasing temperatures, climate change in the Midwest is expected to increase the frequency and intensity of rainstorms (Angel et al. 2018). In Chapter 1, we asked if C. fasciculata has sufficient additive genetic variance for fitness to adapt to extreme rain. We also investigated how extreme rain affects plasticity of, selection on, and heritability of specific leaf area (SLA), a trait thought to mitigate water loss. We manipulated rainfall over a pedigreed population of C. fasciculata using rain shelters and found C. fasciculata possessed a significant capacity to adapt to anomalously wet environments. We also found plants to have thinner leaves in wet environments while selection favored thicker leaves, but fitness remained above replacement (mean lifetime fitness > 1, indicating population growth). In Chapter 2 we asked if C. fasciculata possesses the capacity to adapt to climate change, and how well predictions of the rate of adaptation match what is realized in the field. We planted a pedigreed population of C. fasciculata into three sites along an east to west aridity gradient. The eastern (home) site is predicted to have climate similar to the current climate of the western sites in 25-50 years, so comparisons of the rate of adaptation between the home and western sites will give insight into the capacity of this population to adapt to future climates. We detected significant additive genetic variance for fitness in all sites, which implies this population possesses the capacity to adapt to future climates. Predictions of progeny generation mean fitness were greater than what was realized in the field, and the progeny generation was maladapted. However, maladaptation was buffered by the environment at the home and westernmost site, as the fitness of these populations was above replacement. This work suggests C. fasciculata possesses significant genetic variance to adapt in situ to wetter environments, but a change in the selective environment between generations may cause maladaptation. In chapter 3 we used the experimental design of chapter 2 and asked how climate change alters plasticity of, selection on, and heritability of two key traits, SLA and corolla width, to investigate if changes in plasticity or selection on these traits affects the capacity of C. fasciculata to adapt to future climates. We found significant differences in selection on traits between sites, as well as significant selection for thicker leaves and larger flowers across sites. The plastic response was generally maladaptive (thinner leaves and smaller flowers). We did not find traits to be heritable, which may be a consequence of limited power. Mean fitness in the western most site was above replacement which implies adaptive phenotypic plasticity and adaptive evolution of SLA and corolla width may not be necessary for this population to increase in mean fitness. We detected abundant and significant additive genetic variance for mean lifetime fitness which suggests the populations of C. fasciculata used in this research possess the capacity to adapt to wetter environments. However, temporal environmental variation caused alleles selected by the environment in the parental generation to change frequency in a maladaptive direction, according to the environment in the progeny generation. While the progeny generation was maladapted, mean fitness remained above replacement which is a consequence of plasticity, not adaptive evolution. Mean fitness above replacement at the western most site suggests that this population of C. fasciculata may be able to persist in future climates without seed from other sites. However, the ability of plasticity to buffer populations from environmental change in the long term, as well as the long-term effects of fluctuating selection for demography and evolution, remain unclear and are future research directions. More studies employing the Fundamental Theorem of Natural Selection (FTNS) are needed so we can increase our predictive power of the adaptive capacity of populations in hopes of conserving populations at risk of extinction from climate change.
The hidden costs of rapid adaptation: experimentally assessing the effects of standing variation on the pace and trajectory of evolution
(2022-03) Griffin, Josie
As the planet changes at an alarming rate, there is a great need to understand why some populations are better equipped to rapidly adapt to their new environment than others. Many factors contribute, but populations are ultimately limited in their pace by their genetic makeup—they either have variants that allow them to survive or they do not. But, in the race to adapt, all sources of variation are not equal, and standing genetic variation is theorized to be of the most benefit in contributing to rapid adaptation. Here I explore the role of standing variation, both in a population’s ability to adapt at a rapid pace and in the potential long term evolutionary consequences that occur as a result. My work confirms expectations that increased standing variation in a population allows for a faster rate of adaptation, but although these populations are able to succeed in the short term, but this achievement comes at a significant cost to long term viability. All populations, across all experiments, that utilize standing variation as the genetic basis for rapid adaptation lose the ability to undergo sexual recombination, and therefore lose an important mechanism for maintaining variation in the long term. I begin by determining how the amount of standing variation present in a population correlates to the timing and rate of a successful adaptive response to a stressful environment. I assess how this result is intertwined with loss of sex and explore the mechanism for that loss. Then, I explore how the dynamics of the system change if the environmental shift occurs gradually rather than as a dramatic climactic event. Finally, I compare the variety of evolutionary strategies that develop in populations that began with standing variation versus mutation as their genetic substrate and evaluate their potential for success in the long term. Taken together, these results present a different picture of the role of standing variation than might be assumed. It does indeed allow for rapid adaptation, but the increased degree of genetic variation is not an evolutionary panacea and may send populations down evolutionary trajectories that are short-sighted.
Immunological selection as a driver of porcine reproductive and respiratory syndrome virus (PRRSV) evolution
(2016-07) Wang, Xiong
Porcine reproductive and respiratory syndrome (PRRS) is still one of the most devastating swine infectious diseases worldwide since its initial outbreak in the late 1980s. Its etiologic agent, PRRS virus (PRRSV), is a single strand RNA virus that belongs to the order of Nidovirales, family Arteriviridae and genus Arterivirus. PRRSV is small, viral partial size is about 53nm including a RNA genome with the size of ~ 15kb. PRRSV is highly host restricted to porcine monocyte cells. Currently in the field, biosecurity and passive immunization are the major solutions to reducing the impact of PRRSV endemic. Yet two major factors, the rapidly evolution of PRRSV and the incomplete and highly variable cross-protection induced by passive vaccination, heavily contribute to the penetration of PRRSV to swine herds and result in the emergence and re-emergence of virulent PRRSV. Similar to other RNA virus like human immunodeficiency virus 1 (HIV-1), hepatitis C virus (HCV) and foot-and-mouth disease virus (FMDV), the lack of error prone mechanism during viral replication leads to the production of tremendous mutations in PRRSV progeny. The selection pressure of porcine intrinsic, innate and adaptive immunity on PRRSV population helps shape and drive PRRSV mutation direction. Together, they drive PRRSV’s rapid evolution. Yet there is a limitation in systemic understanding how genetic variation is generated and what selection forces drive PRRSV evolution. The overall objective of this dissertation was to characterize PRRSV evolution in intra-population and field level, as well as exploring the driving forces hidden in the porcine monocyte cells by utilizing high- throughput sequencing and bioinformatics. The findings herein built up an optimized standard protocol to assemble PRRSV whole genome from high-throughput sequencing yields, which can be broadly adapted to other highly-mutated RNA virus. PRRSV infectious clones, similar to field isolates, exist as quasispecies, its population diversity was decreasing under consistent selection pressure of permissive cell intrinsic selection yet retaining significant diversified progeny. In this thesis, an emerging virulent PRRSV in vaccinated herds was identified as a recently evolved member of virulent lineage instead of new virulent strain via built comprehensive and standard analysis pipeline. IFNs and IFN-induced ARFs are highly induced in PAMs after PRRSV inoculation; potential causative key pathways were identified in the PAM age-dependent susceptibility difference scenario. Putting together, all the findings and results provided an improved systematic insight of PRRSV evolution and host innate response, which is a vital immunological selection driver. Ultimately, a better understanding of PRRSV evolution and its driver will lead to a more effective disease prevention, control and elimination.
Reconceptualizing Cancer: The development of new models and frameworks
(2018-12) Liu, Katherine
Cancer research secures an enormous amount of money each year, and researchers are generally quite productive with that money. The trend over the recent years has been for cancer biologists to focus on understanding the early stages of cancer and through a molecular and mechanistic framework. This gets translated into clinical applications through implementation of preventive and screening practices and early treatments. This work is important and has undoubtedly saved many lives. However, metastasis (the spread of cancer throughout the body) is the pathogenic aspect of cancer, and the cause of most cancer-related deaths. We have little ability to successfully treat cancers once they have reached this stage. Thus, this dissertation offers three novel models (two conceptual models and one empirical model) that facilitate the shift of attention away from the elucidation of tumor initiation and early stage cancers to the investigation of metastatic cancers. This shift to metastatic cancers involves more than a temporal shift in the cancer progression. That is, part of my argument is that we cannot simply apply the same conceptual frameworks and methods used to study tumorigenesis but to metastatic cells. Metastasis is more complex than tumor growth, so we need different conceptual models to guide that research. This dissertation begins with a pair of conceptual models, that I argue engage with important causal factors not contained in the molecular and mechanistic frameworks used to study tumorigenesis. I then use a simple model (budding yeast, Saccharomyces cerevisiae) and experimental evolution to empirically validate one of the models that suggests changes in interactions between levels of organization are causally informative in understanding the evolution of a trait (e.g., the evolution of cancer). This work explores how mitochondrial defection is involved in the evolution of tolerance to heat shock, which I use as proof of concept that one needs to consider multiple levels of organization together to understand cancer. In other words, this interdisciplinary dissertation demonstrates how context matters both in interpreting data and setting up research questions. The models I present here may help interpret existing data but also encourage novel research programs such as the empirical work presented here.
The spatial scale of adaptation in common ragweed (Ambrosia artemisiifolia)
(2019-09) Gorton, Amanda
Environmental variation at both large and small spatial scales can influence the ecological and evolutionary trajectory of plant populations. Decades of common garden and reciprocal transplant experiments have demonstrated that local adaptation is widespread. However, most experiments examining local adaptation compare populations at a single spatial scale. For my dissertation, I combined field experiments and population genetics to examine how environmental variation at three spatial scales—small (i.e., among populations), regional (i.e., urban vs. rural), and continental (i.e., across latitudes)—shapes local adaptation in common ragweed (Ambrosia artemisiifolia L.). I found evidence for adaptation to urban environments and latitudinal gradients in climate. More specifically, I found evidence that phenotypic divergence at small spatial scales (e.g. within a city) can be greater than divergence found at larger spatial scales. Across latitudes, I found that photoperiod influences the fitness of common ragweed populations, and the relevant spatial scale for adaptation varies across life history stages. In addition, for northern populations of ragweed, I found that climate change is already causing maladaptation. Lastly, my population genomic work with RNA-seq identified new traits of interest that may be involved in local adaptation, including stomatal opening and closing and seed dormancy. I discuss these results with regard to how they can help us understand local adaptation more broadly and in turn predict how plants may respond to climate change.

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Browsing by Subject "evolution"