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Colorado State University
1.
Chong, Rebecca A.
Complex evolution of mitochondrial genomes: lessons from salamanders.
Degree: PhD, Biology, 2014, Colorado State University
URL: http://hdl.handle.net/10217/83719 
► This dissertation research on genome evolution focuses on understanding the mechanisms that drive the evolution of mitochondrial genome size, content, and organization in animals. This…
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▼ This dissertation research on genome evolution focuses on understanding the mechanisms that drive the evolution of mitochondrial genome size, content, and organization in animals. This research uses a combination of empirical and computational approaches to examine the evolution of mitochondrial genomes in vertebrates, focusing on salamanders as an exemplar clade. Chapter One analyzes mitochondrial genome sequences of vertebrate lineages that differ in metabolic rates. Salamanders, which have the lowest metabolic requirements among tetrapods, experience weaker purifying selection on protein-coding sequences than do frogs, a comparable amphibian clade with higher metabolic rates. In contrast, there is no evidence for weaker selection against mitochondrial genome expansion in salamanders. Together, these results suggest that different aspects of mitochondrial genome evolution (i.e. nucleotide substitution, accumulation of non-coding sequences) are differently affected by metabolic variation across tetrapod lineages. Chapter Two describes the correlation between gene rearrangement/genome expansion and increased rates of substitution in salamander mitochondrial genomes. Most protein-coding genes maintain their position along the mutation gradient in rearranged/expanded mitochondrial genomes, and the genes that do move are unaffected by their new position because the mutation gradient in salamanders is weak. Additionally, genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, these results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes. Chapter Three reports the phylogenetic relationships among lineages of Aneides, sampling both within and among all six species, based on three nuclear markers and describes mitochondrial genome sequences for nine of the taxa represented in the phylogeny. Mitochondrial gene order and level of mitochondrial sequence divergence were estimated for these sequences and two previously published sequences. Two genome duplication events resulting in mitochondrial gene rearrangements were detected, the first rearrangement occurring in the common ancestor of Aneides and the second rearrangement existing across different populations of a single species, A. hardii. Comparisons of A. hardii genomes show that duplicated protein-coding and rRNA genes are lost more rapidly than other duplicated mitochondrial sequence (i.e. tRNAs, non-coding sequence) and suggests that these large scale changes can occur across very shallow levels of genetic divergence.
Advisors/Committee Members: Mueller, Rachel L. (advisor), Webb, Colleen T. (committee member), Funk, W. Chris (committee member), McKay, John K. (committee member).
Subjects/Keywords: gene duplication; molecular evolution; mutation; natural selection; genomics
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APA (6th Edition):
Chong, R. A. (2014). Complex evolution of mitochondrial genomes: lessons from salamanders. (Doctoral Dissertation). Colorado State University. Retrieved from http://hdl.handle.net/10217/83719
Chicago Manual of Style (16th Edition):
Chong, Rebecca A. “Complex evolution of mitochondrial genomes: lessons from salamanders.” 2014. Doctoral Dissertation, Colorado State University. Accessed January 23, 2021.
http://hdl.handle.net/10217/83719.
MLA Handbook (7th Edition):
Chong, Rebecca A. “Complex evolution of mitochondrial genomes: lessons from salamanders.” 2014. Web. 23 Jan 2021.
Vancouver:
Chong RA. Complex evolution of mitochondrial genomes: lessons from salamanders. [Internet] [Doctoral dissertation]. Colorado State University; 2014. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/10217/83719.
Council of Science Editors:
Chong RA. Complex evolution of mitochondrial genomes: lessons from salamanders. [Doctoral Dissertation]. Colorado State University; 2014. Available from: http://hdl.handle.net/10217/83719
Colorado State University
2.
Sheth, Seema Nayan.
Determinants of geographic distribution in western North American monkeyflowers.
Degree: PhD, Ecology, 2014, Colorado State University
URL: http://hdl.handle.net/10217/83815
► The geographic range of a species represents the basic unit of biogeography. Despite ample evidence that properties of geographic ranges vary among species, we do…
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▼ The geographic range of a species represents the basic unit of biogeography. Despite ample evidence that properties of geographic ranges vary among species, we do not fully understand the ecological and evolutionary processes underlying these patterns, thereby hindering our ability to forecast changes in species' distributions in response to changing environments. Key hypotheses about variation in geographic range size among species emphasize the roles of ecological niche properties and the connectivity of suitable habitat. In the first study of my dissertation, I combined primary occurrence data with climate variables to test the relative importance of these hypotheses in 72 species of western North American monkeyflower (genus Mimulus). Climatic niche breadth, via its effect on the amount of suitable habitat, was a strong predictor of geographic range size, whereas climatic niche position (relative to regional climate) and connectivity of climatically suitable habitat were not. Given the role of climatic niche breadth in shaping geographic range sizes in Mimulus, the goal of the second study of my dissertation was to examine the relationship between thermal tolerance (an important axis of niche breadth) and range size experimentally using 5 pairs of closely related Mimulus species with differing range sizes. Within four species pairs, the more geographically widespread species had a broader thermal tolerance than the narrowly distributed species, providing further support for the hypothesis that species with broader niches are able to achieve larger geographic ranges. Further, within each species pair, the species with broader thermal tolerance encompassed greater variation in temperature across its geographic range and higher genetic variation for thermal tolerance than the species with narrower thermal tolerance, supporting the hypotheses that climatic variability and genetic variation in ecologically important traits can explain variation in environmental tolerance among species. Although species vary in range size, every species has a limited geographic range, leading to the question of what prevents a species from expanding its range via niche evolution. Thus, in the third study of my dissertation, I tested whether adaptation at geographic range margins is constrained by insufficient evolutionary potential. To do so, I used artificial selection experiments to quantify genetic variation in flowering time for populations from the northern edge, center, and southern edge of the geographic range of the scarlet monkeyflower (M. cardinalis). Contrary to prediction, southern populations exhibited significantly greater responses to selection (and thus evolutionary potential) than northern or central populations. Together, these results highlight an important role of niche breadth in explaining variation in geographic range size among species, and reveal variation in evolutionary potential that facilitates niche and range expansion within and among species.
Advisors/Committee Members: Angert, Amy L. (advisor), Funk, W. Chris (committee member), McKay, John K. (committee member), Mueller, Rachel L. (committee member), Steingraeber, David (committee member).
Subjects/Keywords: biogeography; Mimulus; niche; thermal tolerance; evolutionary ecology; geographic range
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APA (6th Edition):
Sheth, S. N. (2014). Determinants of geographic distribution in western North American monkeyflowers. (Doctoral Dissertation). Colorado State University. Retrieved from http://hdl.handle.net/10217/83815
Chicago Manual of Style (16th Edition):
Sheth, Seema Nayan. “Determinants of geographic distribution in western North American monkeyflowers.” 2014. Doctoral Dissertation, Colorado State University. Accessed January 23, 2021.
http://hdl.handle.net/10217/83815.
MLA Handbook (7th Edition):
Sheth, Seema Nayan. “Determinants of geographic distribution in western North American monkeyflowers.” 2014. Web. 23 Jan 2021.
Vancouver:
Sheth SN. Determinants of geographic distribution in western North American monkeyflowers. [Internet] [Doctoral dissertation]. Colorado State University; 2014. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/10217/83815.
Council of Science Editors:
Sheth SN. Determinants of geographic distribution in western North American monkeyflowers. [Doctoral Dissertation]. Colorado State University; 2014. Available from: http://hdl.handle.net/10217/83815
3.
Womack, Molly Corinne.
Evolution of 'earlessness' in the true Toad family (Bufonidae), The.
Degree: PhD, Biology, 2016, Colorado State University
URL: http://hdl.handle.net/10217/178880
► Anurans (frogs and toads) have a tympanic middle ear to transmit airborne sound from the environment to their inner ear sensory cells. Yet, many bufonid…
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▼ Anurans (frogs and toads) have a tympanic middle ear to transmit airborne sound from the environment to their inner ear sensory cells. Yet, many bufonid (true toad) species have independently evolved earlessness, the lack of a tympanic middle ear, despite the importance of acoustic communication in most toad mating systems. My thesis aims to determine why middle ear structures are so evolutionarily labile in the Bufonidae family by comparing development, sensory, and morphological data of eared and earless toads within a phylogenetic context. I show that the middle ear forms very late in the development of toads and takes many months past metamorphosis to become fully functional. Adult earless species are typically less sensitive to high frequency sound and more sensitive to low frequency vibrations compared to eared toads. I also find the skulls of eared and earless are very similar, indicating the middle ear is lost without change to other developmentally or genetically linked skull features. I conclude that alternative hearing pathways allow earless species to retain some hearing sensitivity, and discuss roles for development and behavior in shaping the evolutionary lability of ear structures.
Advisors/Committee Members: Hoke, Kim L. (advisor), Davies, Patricia L. (committee member), Mueller, Rachel L. (committee member), Naug, Dhurba (committee member).
Subjects/Keywords: comparative morphology; earless; sensory loss; developmental constraint; anurans; evolutionary development
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APA (6th Edition):
Womack, M. C. (2016). Evolution of 'earlessness' in the true Toad family (Bufonidae), The. (Doctoral Dissertation). Colorado State University. Retrieved from http://hdl.handle.net/10217/178880
Chicago Manual of Style (16th Edition):
Womack, Molly Corinne. “Evolution of 'earlessness' in the true Toad family (Bufonidae), The.” 2016. Doctoral Dissertation, Colorado State University. Accessed January 23, 2021.
http://hdl.handle.net/10217/178880.
MLA Handbook (7th Edition):
Womack, Molly Corinne. “Evolution of 'earlessness' in the true Toad family (Bufonidae), The.” 2016. Web. 23 Jan 2021.
Vancouver:
Womack MC. Evolution of 'earlessness' in the true Toad family (Bufonidae), The. [Internet] [Doctoral dissertation]. Colorado State University; 2016. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/10217/178880.
Council of Science Editors:
Womack MC. Evolution of 'earlessness' in the true Toad family (Bufonidae), The. [Doctoral Dissertation]. Colorado State University; 2016. Available from: http://hdl.handle.net/10217/178880
Colorado State University
4.
Fischer, Eva Kristin.
Flexibility and constraint in the evolution of gene expression and behavior.
Degree: PhD, Biology, 2015, Colorado State University
URL: http://hdl.handle.net/10217/167165
► Our understanding of how underlying molecular, neural, and physiological mechanisms contribute to phenotypic evolvability remains limited. Central to understanding the evolutionary potential of phenotypes is…
(more)
▼ Our understanding of how underlying molecular, neural, and physiological mechanisms contribute to phenotypic evolvability remains limited. Central to understanding the evolutionary potential of phenotypes is an understanding of the extent to which the mechanisms underlying phenotypic differences are flexible versus constrained. My dissertation takes advantage of the unique evolutionary history of Trinidadian guppies (Poecilia reticulata) to explore patterns of flexibility and constraint at three levels. In the first study of my dissertation, I examined genetic and developmental influences on variation and covariation in a suite of behavioral traits to understand whether correlations among traits constrain adaptation to novel environments. I reared guppies from high- and low-predation source populations in environments with and without predators to mimic native and novel environmental conditions and characterized differences in a suite of 21 behaviors measured in four behavioral assays. I found that behavioral variance and covariance structure were altered in novel environments in a manner that likely shaped subsequent selection. My findings suggest that divergence in a novel environment was not constrained by trait correlations in the native environment, and that plastic changes in covariance structure may in fact influence the form of adaptation. In the second study of my dissertation I examined associations between gene expression (transcriptomic) differences and behavior to understand how underlying transcriptional mechanisms mediate behavioral flexibility across developmental and evolutionary timescales. I reared guppies and assayed behavior as before, and quantified whole-brain gene expression from each individual. My dataset allowed me to relate changes in the expression of single genes and gene networks to behavior across genetic backgrounds and rearing environments. I found that conserved gene networks had flexible relationships with behavior, suggesting that alternative transcriptional solutions may give rise to similar behavioral phenotypes across timescales. I propose that this combination of conservation and flexibility balances phenotypic robustness and evolvability in novel environments. Recent studies have considered whether similar phenotypes also share underlying mechanisms, but data are conflicting. In the third study of my dissertation, I compared gene expression signatures associated with adaptation in two distinct evolutionary lineages to ask whether parallel, independent evolutionary events rely on shared mechanisms. I used transcriptomic approaches to quantify genetic and developmental differences in brain gene expression in two high- and low-predation guppy population pairs that represent distinct evolutionary lineages. I found evidence for both shared and distinct transcriptional mechanisms associated with adaptation. Moreover, I demonstrated that expression differences are more likely to evolve in genes that were highly connected to other genes in a gene network.…
Advisors/Committee Members: Hoke, Kim L. (advisor), Ghalambor, Cameron K. (committee member), Hentges, Shane T. (committee member), Mueller, Rachel L. (committee member).
Subjects/Keywords: flexibility; behavior; transcriptomics; neuroethology; Poecilia reticulata
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APA (6th Edition):
Fischer, E. K. (2015). Flexibility and constraint in the evolution of gene expression and behavior. (Doctoral Dissertation). Colorado State University. Retrieved from http://hdl.handle.net/10217/167165
Chicago Manual of Style (16th Edition):
Fischer, Eva Kristin. “Flexibility and constraint in the evolution of gene expression and behavior.” 2015. Doctoral Dissertation, Colorado State University. Accessed January 23, 2021.
http://hdl.handle.net/10217/167165.
MLA Handbook (7th Edition):
Fischer, Eva Kristin. “Flexibility and constraint in the evolution of gene expression and behavior.” 2015. Web. 23 Jan 2021.
Vancouver:
Fischer EK. Flexibility and constraint in the evolution of gene expression and behavior. [Internet] [Doctoral dissertation]. Colorado State University; 2015. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/10217/167165.
Council of Science Editors:
Fischer EK. Flexibility and constraint in the evolution of gene expression and behavior. [Doctoral Dissertation]. Colorado State University; 2015. Available from: http://hdl.handle.net/10217/167165
5.
Siers, Shane Robert.
Microgeographic and ontogenetic variability in the ecology of invasive Brown Treesnakes on Guam, and effects of roads on their landscape-scale movements.
Degree: PhD, Ecology, 2015, Colorado State University
URL: http://hdl.handle.net/10217/166873
Subjects/Keywords: invasive species; ontogenetic variation; road ecology; microgeographic variation; population characteristics; Boiga irregularis
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APA ·
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MLA ·
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CSE |
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APA (6th Edition):
Siers, S. R. (2015). Microgeographic and ontogenetic variability in the ecology of invasive Brown Treesnakes on Guam, and effects of roads on their landscape-scale movements. (Doctoral Dissertation). Colorado State University. Retrieved from http://hdl.handle.net/10217/166873
Chicago Manual of Style (16th Edition):
Siers, Shane Robert. “Microgeographic and ontogenetic variability in the ecology of invasive Brown Treesnakes on Guam, and effects of roads on their landscape-scale movements.” 2015. Doctoral Dissertation, Colorado State University. Accessed January 23, 2021.
http://hdl.handle.net/10217/166873.
MLA Handbook (7th Edition):
Siers, Shane Robert. “Microgeographic and ontogenetic variability in the ecology of invasive Brown Treesnakes on Guam, and effects of roads on their landscape-scale movements.” 2015. Web. 23 Jan 2021.
Vancouver:
Siers SR. Microgeographic and ontogenetic variability in the ecology of invasive Brown Treesnakes on Guam, and effects of roads on their landscape-scale movements. [Internet] [Doctoral dissertation]. Colorado State University; 2015. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/10217/166873.
Council of Science Editors:
Siers SR. Microgeographic and ontogenetic variability in the ecology of invasive Brown Treesnakes on Guam, and effects of roads on their landscape-scale movements. [Doctoral Dissertation]. Colorado State University; 2015. Available from: http://hdl.handle.net/10217/166873
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