Theses and Dissertations at Montana State University (MSU)

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Evolutionary consequences of gene flow in the absence or inhibition of dispersal in microbial communities
(Montana State University - Bozeman, College of Agriculture, 2023) Munro-Ehrlich, Robert Mason; Chairperson, Graduate Committee: Jovanka Voyich-Kane; This is a manuscript style paper that includes co-authored chapters.
Much of our understanding of the evolutionary dynamics of microbial populations is derived from population level studies which focus on the immediately present populations and ignore the contributions of nearby communities. Microbial ecology studies typically do not distinguish between gene flow, i.e., the movement of genetic material between populations, and dispersal, i.e., the movement of those populations themselves. These two processes are indeed linked, but not identical. We have known for centuries that genetic material can be transferred between physically distant and taxonomically disparate microbial populations; molecular biology tools like cloning are dependent on this capability. In other words, gene flow can occur even without dispersal. However, our ecological and evolutionary studies of microbial populations typically fail to acknowledge the evolutionary impact and genetic contributions of outside populations. Unique evolutionary scenarios arise when dispersal between two or more populations is prevented or limited, but gene flow can still occur between them. We hypothesized that this scenario would impact microbial populations by facilitating speciation, selection, and local adaptation. We aimed to test this hypothesis by studying endemic Meiothermus populations inhabiting serpentinite rocks in the subsurface of the Samail ophiolite in Oman. Samail Ophiolite microbial communities, of which Meiothermus populations are a component, are dispersed across the subsurface and separated by meters of solid rock and by chemical and pH gradients spanning orders of magnitude. Despite barriers to dispersal that are significant enough to shape community structure, we found that gene flow still occurred between nearly all observed populations of Meiothermus. This gene flow is contributing to disruptive selection amongst cohabiting populations, and may also be contributing to local adaptation, both at the genetic and genomic level. We also identified potential mechanisms for this gene flow, including abundant viral elements. The sequence similarity of mobile genetic elements in these Meiothermus populations implies that this gene flow occurred after colonization by a common Meiothermus ancestor and that diversification is likely ongoing. To our knowledge, this is the first demonstration of gene flow across barriers to dispersal in an environmental microbial system. In conclusion, these results suggest that the capacity for microbial populations to undergo gene flow even in the absence or inhibition of dispersal is a natural process, has substantial consequences for the evolution of the effected population, and may also have consequences for the microbial and surrounding environment.
The evolution of the chemical abundance gradients in the merging Magellanic Cloud dwarf galaxies
(Montana State University - Bozeman, College of Letters & Science, 2023) Povick, Joshua Tyler; Chairperson, Graduate Committee: David L. Nidever; This is a manuscript style paper that includes co-authored chapters.
Dwarf galaxies are some of the most abundant objects in the Universe, but most of them are very distant and very faint. While observing these galaxies does pose some challenges, they are important to study because it is believed that larger galaxies, such as the Milky Way (MW), form from a series of dwarf mergers in a process called hierarchical merging. As if by chance, the Magellanic Clouds (MCs) are both bright enough and close enough to resolve individual stars. These two dwarf satellites of the MW are also in the process of merging together, presenting a great opportunity to examine how the abundance gradients of galaxies are impacted by intergalactic interactions. A great tool to study the MCs is the Apache Point Galactic Evolution Experiment (APOGEE). APOGEE is an H-band near infrared survey commissioned to measure chemical abundances and accurate radial velocities of the MW and its neighborhood. In the MCs, APOGEE was able to observe 6130 red giant branch (RGB) stars in the Large Magellanic Cloud (LMC) and 2062 RGB stars in the Small Magellanic Cloud (SMC). Individual stellar ages are derived using multiband photometry and spectroscopic parameters to compare to stellar isochrones. Using the abundance measurements of 20+ elements and the derived stellar ages, abundance gradients and their evolutions are extracted from radial abundance trends. The stellar ages in the LMC reveal that recent star formation has been concentrated in the center of that galaxy. The fields that overlay a spiral arm in the north of the LMC reveal median ages of ?2 Gyr. The age-metallicity relation (AMR) remains mostly flat with the exception of an increase in overall metallicity ?2 Gyr ago. Looking at the evolution of many abundance gradients in the LMC there is a U-shaped trend with an extremum around the same time as the increase in metallicity. Additionally, the SMC also shows a U-shaped trend in its abundance gradient evolutions albeit a few billion years earlier than the LMC. These results all correspond to a conjectured close interaction between the LMC and SMC in the recent past.
The relationship of formal reasoning, motivation, and conceptual change: a quantitative study of introductory biology students across the United States
(Montana State University - Bozeman, College of Education, Health & Human Development, 2018) Bernard, Romola Alaica; Chairperson, Graduate Committee: Carrie B. Myers; Steven Kalinowski (co-chair)
There is a noticeable disconnect between conceptual change research carried out in different domains of knowledge. This is starkly apparent in the divide between theoretical models of conceptual change stemming from cognitive and educational psychology, and empirical studies on conceptual change rooted in science education. This study operationalized models of conceptual change that accounted for the rational aspect of conceptual change that dominates in the natural sciences, and the extrarational aspects of conceptual change that are focal in the social sciences. Mixed effects models of conceptual change were investigated. In addition to prior knowledge, formal reasoning ability was incorporated as a critical rational aspect of conceptual change. Academic motivation, plus the teaching and learning environment students experience were included as essential extrarational aspects of conceptual change. The final operational model of conceptual change has post-instruction score as the response variable, and pre-instruction score, formal reasoning ability, intrinsic motivation, representation of racial group in science, teacher experience, and teaching practice as the most important predictors of conceptual change. Prior knowledge and formal reasoning ability are by far the strongest predictors of improving post-instruction conceptual understanding of evolution by natural selection for introductory biology students. There are two noteworthy findings. One, a crucial student characteristic, formal reasoning ability, has been ignored in conceptual change research. When formal reasoning ability is included as a predictor, self-efficacy is not at all important in predicting conceptual change. Two, another student characteristic, race, plays an important role in predicting conceptual change.
Exploring the origin of the Magellanic periphery with SMASH photometric metallicities
(Montana State University - Bozeman, College of Letters & Science, 2019) Miller, Amy Elizabeth; Chairperson, Graduate Committee: David L. Nidever
The distribution of stellar metallicities across the Large and Small Magellanic Clouds is a key ingredient to understanding the processes that have shaped their evolution, and remains a rich ground for exploration. I use data from the Survey of Magellanic Stellar History (SMASH), a photometric survey of the Magellanic Clouds that contains approximately 400 million objects in 197 fields that were obtained with DECam on the CTIO Blanco 4m telescope. SMASH covers 2400 square degrees to 24th magnitude in ugriz, encompassing a depth of 2 magnitudes below the oldest main-sequence turnoff stars. The DECam u-band is sensitive to metallicity for main-sequence turn-off stars, which is calibrated using SDSS and LAMOST spectroscopy in overlapping regions. This analysis is used to make accurate metallicity maps of the main bodies of the Clouds and their peripheries. Ultimately, these metallicity maps will help us trace out population gradients in the Clouds and uncover the origin of their very extended stellar peripheries.
Evolution and function of flavin-based electron bifurcation
(Montana State University - Bozeman, College of Letters & Science, 2018) Poudel, Saroj; Chairperson, Graduate Committee: Eric Boyd; John W. Peters (co-chair); Eric C. Dunham, Melody R. Lindsay, Maximiliano J. Amenabar, Elizabeth M. Fones, Daniel R. Colman and Eric S. Boyd were co-authors of the article, 'Origin and evolution of flavin-based electron bifurcating enzymes' in the journal 'Frontiers in microbiology' which is contained within this thesis.; Amaya M. Garcia Costas was an author and Anne-Frances Miller, Gerrit J. Schut, Rhesa N. Ledbetter, Kathryn R. Fixen, Lance C. Seefeldt, Michael W. W. Adams, Caroline S. Harwood, Eric S. Boyd and John W. Peters were co-authors of the article, 'Defining electron bifurcation in the electron transferring flavoprotein family' in the journal 'Journal of bacteriology' which is contained within this thesis.; Daniel R. Colman was an author and Kathryn R. Fixen, Rhesa N. Ledbetter, Yanning Zheng, Natasha Pence, Lance C. Seefeldt, John W. Peters, Caroline S. Harwood and Eric S. Boyd, were co-authors of the article, 'Electron transfer to nitrogenase in different genomic and metabolic backgrouns' in the journal 'Journal of bacteriology' which is contained within this thesis.
Anaerobic microorganisms live in energy limited environments with low nutrient fluxes. Thus, selection has likely acted on these cells to innovate mechanisms that improve the efficiency of anaerobic energy metabolism. In 2008, the process of flavin-based electron bifurcation (FBEB) was discovered and has since been shown to be a critical process that allows anaerobic cells to overcome thermodynamic barriers and to improve metabolic efficiency. FBEB enzymes catalyze the coupling of exergonic and endergonic oxidation--reduction reactions with the same electron donor to circumvent thermodynamic barriers and minimize free energy loss. To date, a total of 12 FBEB enzymes have been discovered that share common features that include the presence of protein-bound flavin, the proposed site of bifurcation, and the electron carrier ferredoxin. Due to its recent discovery, a comprehensive description of the natural history of bifurcating enzymes is lacking. In this thesis, we report the taxonomic and ecological distribution, functional diversity, and evolutionary history of bifurcating enzyme homologs in available complete genomes and environmental metagenomes. Moreover, we investigated the functional and ecological constraints that led to the emergence of FBEB enzymes. Bioinformatics analyses revealed that FBEB enzyme homologs were primarily detected in the genomes of anaerobes, including those of sulfate-reducers, acetogens, fermenters, and methanogens. Phylogenetic analyses of these enzyme homologs suggest that they were not a property of the Last Universal Common Ancestor of Archaea and Bacteria indicating that they are a more recent evolutionary innovation. Consistent with the role of these enzymes in the energy metabolism of anaerobes, FBEB homologs were enriched in metagenomes from subsurface environments relative to those from surface environments. In fact, the earliest evolving homologs of most bifurcating enzymes were detected in subsurface environments, including fluids from subsurface rock fractures and hydrothermal systems. Together, these data highlight the central role that FBEB played and continued to play in the energy metabolism of anaerobic microbial cells inhabiting subsurface environments.
Dinosaurs and time: chronostratigraphic frameworks and their utility in analysis of dinosaur paleobiology
(Montana State University - Bozeman, College of Letters & Science, 2016) Fowler, Denver Warwick; Chairperson, Graduate Committee: John R. Horner; John B. Scannella and John R. Horner were co-authors of the article, 'Transitional evolutionary forms and stratigraphic trends in Chasmosaurine ceratopsid dinosaurs' which is contained within this dissertation.; Holly N. Woodward, Elizabeth A. Freedman, Peter L. Larson and John R. Horner were co-authors of the article, 'Reanalysis of 'Raptorex kriegsteini': a juvenile tyrannosaurid dinosaur from Mongolia' in the journal 'PLOS ONE' which is contained within this dissertation.; This dissertation contains two articles of which Denver W. Fowler is not the main author.
Stratigraphy is the study of the position of rock strata, in order to determine their age. Dinosaur fossils have been recovered from North America for over 150 years, yet the stratigraphy of the localities from which they were collected has rarely been analysed at high resolution, either due to lack of original locality data, or that precise correlation between depositional basins was not technologically possible. This dissertation analyses what effect the introduction of high-resolution chronostratigraphic data has on our understanding of dinosaur paleobiology. Terrestrial sequence stratigraphy was used in combination with previously published data in order to subdivide the uppermost Cretaceous Hell Creek Formation of Montana into lower, middle, and upper units, shown to be consistent across the formation type area. Similar stratigraphic data was gathered for each of the Late Cretaceous dinosaur-bearing formations of the North American Western Interior, which was combined with nearly 200 radiometric dates (newly recalibrated here) to plot a comprehensive high-resolution correlation chart. The stratigraphic occurrence of dinosaur taxa was consequently plotted upon this chart. Similarly, the new Hell Creek Formation stratigraphic framework was used to plot the stratigraphic occurrence of Triceratops fossils. From this it can be seen that many dinosaur groups form stacks of stratigraphically separated species, a pattern indicative of linear, non-branching evolution (anagenesis). A similar pattern is observed for two new taxa of chasmosaurine ceratopsid (horned) dinosaurs from New Mexico, which form morphologic and stratigraphic intermediates between the slightly older taxon, Pentaceratops, and the younger Anchiceratops. Phylogenetic and geometric morphometric analysis supports the hypothesis that the posterior embayment of the parietal deepens and closes in on itself over ~ 2 million years from Pentaceratops through the new taxa, to Anchiceratops, and suggests a deep split within Chasmosaurinae that occurs before the Middle Campanian. These findings imply that dinosaur evolution in the Late Cretaceous Western Interior was characterized mostly by anagenesis, punctuated by occasional speciation events, perhaps triggered by high sealevel creating a north / south geographic barrier. The evolutionary process of reinforcement is discussed as a possible mechanism for the development of cranial display organs, linked to speciation.
Impact of Chukwin-mini unit on students' understanding of natural selection
(Montana State University - Bozeman, Graduate School, 2016) Bauer, Sarah Elizabeth; Chairperson, Graduate Committee: Peggy Taylor.
Instruction on evolution can be fraught with controversy, which may lead to teachers avoiding it and students struggling to learn it. Yet it is national science standard, a foundation in the field of biology, and a key to science literacy. A constructivist mini-unit incorporating simulation-based games involving a population of imaginary creatures called Chukwins was created to maximize student learning and minimize tension. It was tested in an elementary, junior high, and high school classrooms in three different locations. Changes in understanding were assessed with pretest/posttest data. Surveys and interviews provided additional evidence on students' attitudes towards the mini-unit, its impact on learning and engagement, and understanding of evolution. Students made statistically significant improvements on assessments regarding natural selection, reducing their number of misconceptions and slightly improving their ability to apply correct concepts. Retention scores indicate that the changes, though small, are long-lasting. Little change was found in students' attitudes towards evolution after treatment. The vast majority of students viewed the mini-unit favorably and found it to be a valuable learning opportunity, which was echoed by the classroom teachers. The mini-unit could be a valuable tool for teachers in helping students learn about natural selection and evolution in a way that is fun, motivating, and leads to conceptual change even for students with strong opposition to the theory of evolution.
In situ and enhanced coal-bed methane production from the Powder River Basin
(Montana State University - Bozeman, College of Letters & Science, 2014) Barnhart, Elliott Paul; Chairperson, Graduate Committee: Matthew Fields; Kara Bowen De León, Bradley D. Ramsay, Alfred B. Cunningham, and Matthew W. Fields were co-authors of the article, 'Investigation of coal-associated bacterial and archaeal populations from a diffusive microbial sampler (DMS)' in the journal 'International journal of coal geology' which is contained within this thesis.; Bradley D. Ramsay, Kara Bowen De León, Kristen A. Brileya, Denise M. Akob, Richard E. Macur, Alfred B. Cunningham, Matthew W. Fields were co-authors of the article, 'Stimulation of coal-dependent methanogenesis with native microbial consortia from the Powder River Basin' submitted to the journal 'Applied and environmental microbiology' which is contained within this thesis.; Kiki Johnson, Kristopher A. Hunt, Sean Cleveland, Marcella A. McClure, Matthew W. Fields were co-authors of the article, 'Genomic insight into the evolution of the acetate switch in archaea' submitted to the journal 'Nature' which is contained within this thesis.
The majority of the coal in the Powder River Basin (PRB) is located in formations too deep to be economically mined but microorganisms within some of these deep coal seams generate coal-bed methane (CBM) which can be harvested and utilized as an energy source. However, little is known about the in situ microbial community, the environmental conditions conducive to CBM production, or the microbial community interactions that promote CBM production. Several sampling locations within the PRB were identified as methane-producing sites based on geochemical analysis of groundwater. A diffusive microbial sampler (DMS) was utilized for microbial sampling which was loaded with coal and only opened at the bottom of the wells where the coal seam was exposed. Pyrotag analysis of DMS coal identified the predominant in situ bacterial and archaeal populations, providing insight into microbes generating CBM within the PRB. Changes in the composition and structure of microbial communities that occur under stimulated conditions were investigated by applying molecular methods in combination with cultivation techniques (with and without nutrient supplementation) to identify conditions which maximize methane production in batch, bench-scale incubations. Results from these studies indicated the addition of yeast extract resulted in an increase in methane production as well as a shift to a microbial population capable of acetate production and/or acetate utilization. Isolation methods targeting coal utilizing Bacteria and methanogenic Archaea were applied in addition to DNA based methods to infer microbial community members present within coalbeds. The acetoclastic methanogen Methanosarcina was isolated which is the only identified methanogen with the high-efficiency acetate kinase (Ack) / phosphotransacetylase (Pta) methane production pathway. This pathway provides increased growth and methane production when acetate concentrations are high which can result from microbial stimulation with nutrients. Genomic analysis revealed Ack evolved through gene duplication and divergence of acetyl CoA synthetase within the methanogenic genome. This research provided novel insight into the evolution of the high-efficiency Ack/Pta pathway. Collectively, this dissertation presents a novel link between the Ack/Pta pathway, stimulated CBM production and genomic insight into the development of this pathway.
Systematics of Lactarius in the Rocky Mountain alpine zone
(Montana State University - Bozeman, College of Agriculture, 2015) Barge, Edward Gilman; Chairperson, Graduate Committee: Cathy L. Cripps
Lactarius is an important component of the ectomycorrhizal community in cold-dominated arctic and disjunct alpine habitats where it associates primarily with the woody shrubs Betula, Dryas, and Salix. Little is known of the alpine fungi in the central and southern (Montana, Wyoming, Colorado) Rocky Mountain alpine zone (elevation 3,000-3,900 m) of North America. The goal of this study was to examine the genus Lactarius and here at least six species from subgenera Russlularia and Piperites are confirmed above treeline through molecular phylogenetic analyses of ITS and rpb2 DNA in conjunction with detailed morphological examination. All (except two putative new species) appear to have broad intercontinental distributions in North America and Eurasia according to molecular comparison with type material, and collections from Europe, Greenland, Scandinavia, Svalbard, and Alaska. Rocky Mountain alpine collections of L. lanceolatus and the type from Alaska form a well-supported clade paraphyletic with respect to well-supported clades consisting of L. aurantiacus and several North American subalpine taxa. Rocky Mountain alpine collections of L. nanus, L. glyciosmus, L. repraesentaneus, and L. salicis-reticulatae all form well-supported clades with material from European type localities and other arctic-alpine material; although some clades contain nested (L. hysginoides within L. nanus) and possibly cryptic species (L. aff. salicis-reticulatae from Colorado). The well-known arctic-alpine L. pseudouvidus/L. brunneoviolaceus group of violet-staining species appears to be a complex possibly containing additional species. North American material originally described as part of this group, is well-separated phylogenetically and represents a putative new species (L. pallidomarginatus Barge & C.L. Cripps ad int.) so far confined to the Southern Rockies with shrub Salix. The monophyly of the violet-staining section Uvidi is supported. Lactarius lanceolatus, L. nanus, and L. salicis-reticulatae appear largely restricted to arctic-alpine habitats across their broad range, where they associate with dwarf and shrub Salix. Lactarius glyciosmus and L. repraesentaneus are not restricted to arctic-alpine areas and occur with Betula and krummholz Picea (possibly also Salix), respectively in the Rocky Mountains; the latter is also known with Betula in broader parts of its range. Species distributions are hypothesized to be tied to host ranges, glaciation, and long distance dispersal.
Superfluid effects on thermal evolution and rotational dynamics of neutron stars
(Montana State University - Bozeman, College of Letters & Science, 2001) Larson, Michelle Beauvais

Theses and Dissertations at Montana State University (MSU)

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