subject:(molecular evolution)

University of Oxford

1. Dai, Yichen. Weird gene in a weird mammal : comparative and functional analysis of the highly divergent sand rat Pdx1 gene.

Degree: PhD, 2020, University of Oxford

URL: http://ora.ox.ac.uk/objects/uuid:f96af087-c350-4d86-a2f7-315b7ec655a5 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.816672

► Deleterious mutations in highly conserved genes are expected to be removed by natural selection. However, when these genes are trapped in dynamic regions of the… (more)

▼ Deleterious mutations in highly conserved genes are expected to be removed by natural selection. However, when these genes are trapped in dynamic regions of the genome, for example mutational hotspots, it becomes difficult to predict how the conflict between nucleotide changes and natural selection will be resolved. In this thesis, I investigate highly divergent genes in the fat sand rat (Psammomys obesus) associated with GC-skew. To understand how the tug-of-war between GC-skew and natural selection is resolved, I focus on a highly representative example of an extremely conserved gene trapped in an extreme GCrich region of the sand rat genome: pancreatic duodenum homeobox 1 (Pdx1). In Chapter 2, I hypothesize that the highly divergent sand rat PDX1 protein may be a result of adaptive selection, and that similar amino acid changes may be observed in other arid-living rodents. Using genomic and transcriptomic data gathered from 33 rodent species, I show that there is near 100% conservation of the PDX1 homeodomain sequence in non-gerbil species, including 15 rodent species that reside in arid or semi-arid habitats. The highly divergent Pdx1 gene observed in the sand rat is only found in three gerbil species, suggesting that adaptive or relaxed selection in an arid environment may not be the key factor affecting Pdx1 gene evolution in this lineage. Instead, other factors such as GC composition bias may be the main factor driving Pdx1 gene divergence in the gerbil subfamily. In Chapter 3, I hypothesize that natural selection may have only managed to purge extremely deleterious mutations while tolerating the existence of mildly deleterious mutations in these genes. Using mammalian cell transfection and pulse-chase labelling, I reveal loss of a conserved ubiquitination site and compensation from a unique, gerbil-specific ubiquitination site. This provides evidence for loss of a conserved amino acid with important function associated with GC-skew and links the presence of a gerbil-unique lysine residue with a specific function. In Chapter 4, I use qPCR to demonstrate significantly altered regulatory effects of the sand rat PDX1 protein on key target genes in rat pancreatic cells, Ins1 and Ins2. I also present establishment of CRISPR/Cas9 edited knock-in cell lines with the aim of teasing apart whether these observed differences were caused by changes in sand rat PDX1 binding site recognition. I conclude that the highly divergent sand rat PDX1 has likely lost conserved functional residues and has significantly reduced ability to initiate proper biological response to glucose stimulation in a rat cell environment. At the same time, results in Chapter 3 show the presence of gerbil-specific residues with specific function, indicating possible compensation by natural selection. I use genome wide comparison methods in Chapter 5 to demonstrate that extreme GC-skew has affected multiple highly conserved genes with assorted function. Pdx1 is not the only aberrantly divergent gene in the gerbil lineage, and these aberrantly divergent…

Subjects/Keywords: Molecular biology; Zoology; Molecular evolution

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dai, Y. (2020). Weird gene in a weird mammal : comparative and functional analysis of the highly divergent sand rat Pdx1 gene. (Doctoral Dissertation). University of Oxford. Retrieved from http://ora.ox.ac.uk/objects/uuid:f96af087-c350-4d86-a2f7-315b7ec655a5 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.816672

Chicago Manual of Style (16^th Edition):

Dai, Yichen. “Weird gene in a weird mammal : comparative and functional analysis of the highly divergent sand rat Pdx1 gene.” 2020. Doctoral Dissertation, University of Oxford. Accessed March 05, 2021. http://ora.ox.ac.uk/objects/uuid:f96af087-c350-4d86-a2f7-315b7ec655a5 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.816672.

MLA Handbook (7^th Edition):

Dai, Yichen. “Weird gene in a weird mammal : comparative and functional analysis of the highly divergent sand rat Pdx1 gene.” 2020. Web. 05 Mar 2021.

Vancouver:

Dai Y. Weird gene in a weird mammal : comparative and functional analysis of the highly divergent sand rat Pdx1 gene. [Internet] [Doctoral dissertation]. University of Oxford; 2020. [cited 2021 Mar 05]. Available from: http://ora.ox.ac.uk/objects/uuid:f96af087-c350-4d86-a2f7-315b7ec655a5 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.816672.

Council of Science Editors:

Dai Y. Weird gene in a weird mammal : comparative and functional analysis of the highly divergent sand rat Pdx1 gene. [Doctoral Dissertation]. University of Oxford; 2020. Available from: http://ora.ox.ac.uk/objects/uuid:f96af087-c350-4d86-a2f7-315b7ec655a5 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.816672

Rutgers University

2. Seah, Yee Mey. Molecular evolution and phylogenetics of circular single-stranded DNA viruses.

Degree: PhD, Microbiology and Molecular Genetics, 2015, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/48645/

►

Viruses infect a wide variety of hosts across all domains of life. Despite their ubiquity, and a long history of virus research, fundamental questions such… (more)

Subjects/Keywords: Molecular evolution; DNA

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Seah, Y. M. (2015). Molecular evolution and phylogenetics of circular single-stranded DNA viruses. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/48645/

Chicago Manual of Style (16^th Edition):

Seah, Yee Mey. “Molecular evolution and phylogenetics of circular single-stranded DNA viruses.” 2015. Doctoral Dissertation, Rutgers University. Accessed March 05, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/48645/.

MLA Handbook (7^th Edition):

Seah, Yee Mey. “Molecular evolution and phylogenetics of circular single-stranded DNA viruses.” 2015. Web. 05 Mar 2021.

Vancouver:

Seah YM. Molecular evolution and phylogenetics of circular single-stranded DNA viruses. [Internet] [Doctoral dissertation]. Rutgers University; 2015. [cited 2021 Mar 05]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/48645/.

Council of Science Editors:

Seah YM. Molecular evolution and phylogenetics of circular single-stranded DNA viruses. [Doctoral Dissertation]. Rutgers University; 2015. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/48645/

Dalhousie University

3. Alfaro, Javier Antonio. CAPTURING THE DYNAMICS OF PROTEIN SEQUENCE EVOLUTION THROUGH SITE-INDEPENDENT STRUCTURALLY CONSTRAINED PHYLOGENETIC MODELS.

Degree: MS, Department of Biochemistry & Molecular Biology, 2014, Dalhousie University

URL: http://hdl.handle.net/10222/54064

► Protein function arises from the large scaffold of residue interactions that position critical residues to stabilize the fold and to interact with substrates and other… (more)

Subjects/Keywords: Molecular Evolution; Structural Constraint; Neutral Evolution

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Alfaro, J. A. (2014). CAPTURING THE DYNAMICS OF PROTEIN SEQUENCE EVOLUTION THROUGH SITE-INDEPENDENT STRUCTURALLY CONSTRAINED PHYLOGENETIC MODELS. (Masters Thesis). Dalhousie University. Retrieved from http://hdl.handle.net/10222/54064

Chicago Manual of Style (16^th Edition):

Alfaro, Javier Antonio. “CAPTURING THE DYNAMICS OF PROTEIN SEQUENCE EVOLUTION THROUGH SITE-INDEPENDENT STRUCTURALLY CONSTRAINED PHYLOGENETIC MODELS.” 2014. Masters Thesis, Dalhousie University. Accessed March 05, 2021. http://hdl.handle.net/10222/54064.

MLA Handbook (7^th Edition):

Alfaro, Javier Antonio. “CAPTURING THE DYNAMICS OF PROTEIN SEQUENCE EVOLUTION THROUGH SITE-INDEPENDENT STRUCTURALLY CONSTRAINED PHYLOGENETIC MODELS.” 2014. Web. 05 Mar 2021.

Vancouver:

Alfaro JA. CAPTURING THE DYNAMICS OF PROTEIN SEQUENCE EVOLUTION THROUGH SITE-INDEPENDENT STRUCTURALLY CONSTRAINED PHYLOGENETIC MODELS. [Internet] [Masters thesis]. Dalhousie University; 2014. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10222/54064.

Council of Science Editors:

Alfaro JA. CAPTURING THE DYNAMICS OF PROTEIN SEQUENCE EVOLUTION THROUGH SITE-INDEPENDENT STRUCTURALLY CONSTRAINED PHYLOGENETIC MODELS. [Masters Thesis]. Dalhousie University; 2014. Available from: http://hdl.handle.net/10222/54064

Penn State University

4. Rabaa, Maia Anita. The molecular evolution and phylogeography of dengue viruses in Asia.

Degree: 2012, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/16341

► The global burden of dengue and its impact on the health and economics of tropical countries is vast and continues to grow. Outbreaks of severe… (more)

▼ The global burden of dengue and its impact on the health and economics of tropical countries is vast and continues to grow. Outbreaks of severe dengue disease are increasingly common in regions where dengue was thought to be rare only a decade ago. Our knowledge of the epidemiological and evolutionary processes by which dengue viruses (DENV) invade new populations and become established as persistent viral lineages has been limited by a lack of data relating virus to host and vector populations, as well as the immune landscapes in which they spread over time. Virus lineages enter new populations regularly, but become established only occasionally and are generally detected long after establishment has occurred. The introduction of novel viral lineages has been shown to perturb the immune landscape in endemic environments, often causing massive epidemics and long-term changes in clinical manifestations within the host population. The use of large sets of spatially- and temporally- related DENV genome and envelope gene (E) sequences to investigate these lineage establishment events allows us to trace the timing and routes of viral movement between host populations, including the evolutionary dynamics of the viral lineages themselves. Determining whether trends in viral introduction and establishment can be distinguished within DENV phylogenies, and what these trends may be, is integral to understanding and controlling the spread of disease at local, regional, and global scales. In this thesis, I explore the spatio-temporal dynamics of DENV dispersal to identify the routes by which dengue invades new populations, characterize trends in viral migration, and identify the factors that affect the speed and scope of DENV migration at various scales and in heterogeneous transmission environments. In hyperendemic settings, I determined that DENV diversity is maintained in densely populated urban areas, frequently spreading through urban and suburban populations and into rural areas, and following a predictable pattern of human movement that suggests a limited role for the vector in the rapid dispersal of an emerging lineage across the population. Once arriving in rural areas, transmission is remarkably spatially and temporally focal. Where climate conditions are suitable, these populations may show persistence of viral populations over multiple seasons, but the likelihood of lineage fade-out here is increased as a result of lower population densities and seasonal bottlenecks in DENV populations. Hyperendemic urban areas further seed more distant populations at rates that appear to be dependent upon transmission intensities in the donor population and the connectedness of the human host populations, while the establishment of viral populations may show a greater dependence upon the immune landscape and the climate into which the virus is introduced. This is also true at the largest spatial and temporal scales, where I identify three geographic regions in tropical Asia that act as sources of global DENV diversity and suggest… Advisors/Committee Members: Edward C Holmes, Dissertation Advisor/Co-Advisor, Andrew Fraser Read, Committee Chair/Co-Chair, Isabella Cattadori, Committee Member, Timothy Reluga, Committee Member.

Subjects/Keywords: dengue; molecular evolution; phylogeography; virus evolution

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rabaa, M. A. (2012). The molecular evolution and phylogeography of dengue viruses in Asia. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/16341

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Rabaa, Maia Anita. “The molecular evolution and phylogeography of dengue viruses in Asia.” 2012. Thesis, Penn State University. Accessed March 05, 2021. https://submit-etda.libraries.psu.edu/catalog/16341.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Rabaa, Maia Anita. “The molecular evolution and phylogeography of dengue viruses in Asia.” 2012. Web. 05 Mar 2021.

Vancouver:

Rabaa MA. The molecular evolution and phylogeography of dengue viruses in Asia. [Internet] [Thesis]. Penn State University; 2012. [cited 2021 Mar 05]. Available from: https://submit-etda.libraries.psu.edu/catalog/16341.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Rabaa MA. The molecular evolution and phylogeography of dengue viruses in Asia. [Thesis]. Penn State University; 2012. Available from: https://submit-etda.libraries.psu.edu/catalog/16341

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas – Austin

5. -9090-4788. Investigating the behaviors and limitations of phylogenetic models of protein-coding sequence evolution.

Degree: PhD, Ecology, Evolution, and Behavior, 2016, University of Texas – Austin

URL: http://hdl.handle.net/2152/38770

► Probabilistic models which infer the strength and direction of natural selection from protein-coding sequences are among the most widely-used tools in comparative sequence analysis. A… (more)

▼ Probabilistic models which infer the strength and direction of natural selection from protein-coding sequences are among the most widely-used tools in comparative sequence analysis. A variety of phylogenetic models of coding-sequence evolution have been developed. However, these models have been produced independently from one another. As a consequence, it has been entirely unknown whether inferences from different models reveal similar or incompatible information about the evolutionary process. In this dissertation, I derive and study the mathematical relationship between two probabilistic models of protein-coding sequence evolution: dN/dS-based models, which estimate evolutionary rates, and mutation–selection models, which estimate site-specific amino-acid fitnesses. I demonstrate how this relationship reveals the behavioral properties, limitations, and applicabilities of different inference frameworks, which leads to concrete recommendations for how these models should best be employed in evolutionary sequence analysis. In Chapter 2, I develop a flexible and extendable software, implemented as a module in the Python programming language, for simulating sequences along phylogenies according to standard evolutionary models. This software platform provides an independent and user-friendly platform for testing model behavior, or indeed developing novel evolutionary models, thus enabling robust comparisons of modeling frameworks. In Chapter 3, I derive a mathematical relationship between dN/dS and amino-acid fitness values, and I show that mutation– selection models fully encompass information encoded in dN/dS models, provided that sequences are evolving under purifying selection. I further use this relationship to show that certain commonly-used dN/dS-based models are strongly and systematically biased. I additionally show that standard metrics used for model selection in phylogenetics (e.g. Akaike Information Criterion) may be positively misleading and indicate strong support for incorrect models. Finally, in Chapter 4, I apply the mathematical relationship developed in Chapter 3 to study the accuracy of two competing mutation–selection inference implementations, whose relative merits have been heavily debated in the literature. My approach demonstrates that mutation–selection inference platforms that treat amino-acid fitnesses as fixed-effect variables precisely estimate site-specific evolutionary constraints. By contrast, inference platforms that treat fitnesses as random-effect variables systematically underestimate the strength of natural selection across sites. Taken together, the work presented in this dissertation yields novel insights into how these popular evolutionary models can best be applied to sequence data, how their results should be interpreted, and finally how future model development should be conducted in order to yield robust and reliable inference methods. Advisors/Committee Members: Wilke, C. (Claus) (advisor), Bull, James (committee member), Barrick, Jeffrey (committee member), Hillis, David (committee member), Hofmann, Hans (committee member).

Subjects/Keywords: Molecular evolution; Protein evolution; Phylogenetic models

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

-9090-4788. (2016). Investigating the behaviors and limitations of phylogenetic models of protein-coding sequence evolution. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/38770

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

-9090-4788. “Investigating the behaviors and limitations of phylogenetic models of protein-coding sequence evolution.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed March 05, 2021. http://hdl.handle.net/2152/38770.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

-9090-4788. “Investigating the behaviors and limitations of phylogenetic models of protein-coding sequence evolution.” 2016. Web. 05 Mar 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

-9090-4788. Investigating the behaviors and limitations of phylogenetic models of protein-coding sequence evolution. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2152/38770.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

-9090-4788. Investigating the behaviors and limitations of phylogenetic models of protein-coding sequence evolution. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/38770

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Rutgers University

6. Manhart, Michael. Biophysics and stochastic processes in molecular evolution.

Degree: PhD, Physics and Astronomy, 2014, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/45338/

►

Evolution is the defining feature of living matter. It occurs most fundamentally on the scale of biomolecules such as DNA and proteins, which carry out… (more)

▼

Evolution is the defining feature of living matter. It occurs most fundamentally on the scale of biomolecules such as DNA and proteins, which carry out all the processes of cells. How do the physical properties of these molecules shape the course of evolution? We address this question using a synthesis of biophysical models, theoretical tools from stochastic processes, and high-throughput data. We first review some basic features of population and evolutionary dynamics, focusing especially on fitness landscapes and how they determine accessible pathways of evolution. We then derive a universal scaling law describing time reversibility and steady state of monomorphic populations on arbitrary fitness landscapes. We use this result to study the evolution of transcription factor (TF) binding sites using high-throughput data on TF-DNA interactions and genome-wide site locations. We find that binding sites for a given TF appear to be subjected to universal selection pressures, independent of the properties of their corresponding genes, and their binding energy-dependent fitness is consistent with a simple functional form inspired by a thermodynamic model. We next consider the properties of evolutionary pathways. We develop a general approach for calculating statistical properties of the path ensemble in a stochastic process. We first demonstrate this approach on a series of simple examples, including evolution on a neutral network and two reaction rate problems. We then apply these techniques to a model of how proteins evolve new binding interactions while maintaining folding stability. In particular we show how the structural coupling of protein folding and binding results in protein traits emerging as evolutionary "spandrels'': proteins can evolve strong binding interactions that confer no intrinsic fitness advantage but merely serve to stabilize the protein if misfolding is deleterious. These observations may explain the abundance of apparently nonfunctional interactions among proteins observed in high-throughput assays. When there are distinct selection pressures on both folding and binding, evolutionary paths of proteins can be tightly constrained so that folding stability is first gained and then partially lost as the new binding function is developed. This suggests the evolution of many natural proteins is highly predictable at the level of biophysical traits.

Advisors/Committee Members: Morozov, Alexandre V (chair), Sengupta, Anirvan M (internal member), Bhanot, Gyan (internal member), Andrei, Natan (internal member), Chen, Kevin (outside member).

Subjects/Keywords: Molecular evolution; Evolution (Biology); Protein folding

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Manhart, M. (2014). Biophysics and stochastic processes in molecular evolution. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/45338/

Chicago Manual of Style (16^th Edition):

Manhart, Michael. “Biophysics and stochastic processes in molecular evolution.” 2014. Doctoral Dissertation, Rutgers University. Accessed March 05, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/45338/.

MLA Handbook (7^th Edition):

Manhart, Michael. “Biophysics and stochastic processes in molecular evolution.” 2014. Web. 05 Mar 2021.

Vancouver:

Manhart M. Biophysics and stochastic processes in molecular evolution. [Internet] [Doctoral dissertation]. Rutgers University; 2014. [cited 2021 Mar 05]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/45338/.

Council of Science Editors:

Manhart M. Biophysics and stochastic processes in molecular evolution. [Doctoral Dissertation]. Rutgers University; 2014. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/45338/

University of California – Berkeley

7. Young, Susan Louise. The unicellular ancestry of the proto-oncogene Myc.

Degree: Molecular & Cell Biology, 2010, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/5hr0154z

► The origin of metazoans required the evolution of mechanisms of cell-cell adhesion, coordination and communication among neighboring cells, and the establishment of differentiated cell types.… (more)

▼ The origin of metazoans required the evolution of mechanisms of cell-cell adhesion, coordination and communication among neighboring cells, and the establishment of differentiated cell types. Did the molecular building blocks of metazoan multicellularity exist in their single celled ancestors, or are they unique metazoan innovations? To address this question we sequenced and analyzed the genome of the unicellular marine choanoflagellate Monosiga brevicollis. Choanoflagellates, a phylum of flagellated unicellular and colonial eukaryotes found in diverse aqueous habitats around the globe, are among the closest living relatives of metazoans. The roughly 46 million base pair genome of M. brevicollis contains approximately 9,200 unexpectedly intron-rich genes, including a number of genes that encode cell adhesion and signaling protein domains that are otherwise restricted to metazoans. The physical linkages among these domains often differ between M. brevicollis and metazoans suggesting that abundant domain shuffling followed the separation and subsequent diversification of the choanoflagellate and metazoan lineages. Metazoans also have a richer diversity of transcription factors than does M. brevicollis, indicating that the evolution of early metazoans may have involved an increase in the sophistication of transcriptional regulation. Nonetheless, a few metazoan-type transcription factors were identified in M. brevicollis: members of the p53, Myc, and Sox/TCF transcription factor families. Myc is a developmentally critical transcription factor that plays roles in the most fundamental of cellular processes: cell growth, proliferation, and death. Investigating the function of Myc in choanoflagellates promises to delineate the role of Myc before the origin of animals and may inform how the strict regulation of cell life and death in metazoans arose from a unicellular context. Here, we demonstrate M. brevicollis Myc heterodimerizes with M. brevicollis MAX and localizes to the nucleus and cytoplasm of choanoflagellate cells in varying intensity. We further show that the tyrosine kinase (TK) inhibitor genistein reduces the expression of MbMyc, suggesting that TK signaling regulates MbMyc. Because metazoans Mycs are also known to be regulated by TK signaling, we hypothesize that an emergent network of TK signaling and transcriptional regulation was present in the unicellular ancestor of animals.

Subjects/Keywords: Biology, Molecular; choanoflagellate; evolution; myc

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Young, S. L. (2010). The unicellular ancestry of the proto-oncogene Myc. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/5hr0154z

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Young, Susan Louise. “The unicellular ancestry of the proto-oncogene Myc.” 2010. Thesis, University of California – Berkeley. Accessed March 05, 2021. http://www.escholarship.org/uc/item/5hr0154z.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Young, Susan Louise. “The unicellular ancestry of the proto-oncogene Myc.” 2010. Web. 05 Mar 2021.

Vancouver:

Young SL. The unicellular ancestry of the proto-oncogene Myc. [Internet] [Thesis]. University of California – Berkeley; 2010. [cited 2021 Mar 05]. Available from: http://www.escholarship.org/uc/item/5hr0154z.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Young SL. The unicellular ancestry of the proto-oncogene Myc. [Thesis]. University of California – Berkeley; 2010. Available from: http://www.escholarship.org/uc/item/5hr0154z

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Rhodes University

8. Riddin, Megan Amy. Systematics and biogeography of Mesobola brevianalis (Boulenger, 1908) (Teleostei: Cyprinidae).

Degree: Faculty of Science, Zoology and Entomology, 2015, Rhodes University

URL: http://hdl.handle.net/10962/d1017808

► The accurate identification of fish species, their life stages and their products enables the correct management of fisheries, research and conservation of distinctive populations for… (more)

▼ The accurate identification of fish species, their life stages and their products enables the correct management of fisheries, research and conservation of distinctive populations for long-term survival and sustainability. Mesobola brevianalis Boulenger, 1908, commonly known as the river sardine, is found in many river systems in southern Africa. Because it exhibits widely separated populations showing subtle differences, particularly in colour, it is thought that there may be cryptic species involved. Standard phylogenetic techniques using three genetic markers (mitochondrial COI, nuclear protein RAG1 and nuclear ribosomal 28S rRNA), enabled the building of phylogenetic networks for M. brevianalis and some outgroup species. Consistent patterns of relationship were seen with 28S supporting monophyly. COI and RAG1 suggested that populations that are currently identified as M. brevianalis in fact represent several species. There was sufficiently strong support for the evolutionary independence of the M. brevianalis populations from the Rovuma, Kunene and Orange River Systems to consider them as independent species. The independence of the genus Mesobola was brought into question because Engraulicypris sardella and Rastrineobola argentea were placed within it phylogenetically.Morphometric methods in the form of multivariate truss network analyses, were performed to locate morphological markers for populations. There was little to no variation among most of the populations synonymized under M. brevianalis. Furthermore, neither latitude nor longitude had an effect on the morphological characters that might be linked to functional evolution. A molecular clock analysis of COI data was used to calibrate a paleobiogeographical model which entailed a divergence of lineages starting from an easterly reigning Paleo-Congo Basin, via a hypothetical Paleo-Kalahari Lake that was fragmented by a series of uplifts and drying events beginning ~65 million years ago. Complete evidence supported the synonymisation of the genera Engraulicypris and Mesobola, the resurrection of the species name gariepinus for the Orange River Systempopulation, and the description of two new species: E. ngalala from the Rovuma River System and E. howesi from the Kunene River System.

Subjects/Keywords: River sardine; Molecular evolution

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Riddin, M. A. (2015). Systematics and biogeography of Mesobola brevianalis (Boulenger, 1908) (Teleostei: Cyprinidae). (Thesis). Rhodes University. Retrieved from http://hdl.handle.net/10962/d1017808

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Riddin, Megan Amy. “Systematics and biogeography of Mesobola brevianalis (Boulenger, 1908) (Teleostei: Cyprinidae).” 2015. Thesis, Rhodes University. Accessed March 05, 2021. http://hdl.handle.net/10962/d1017808.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Riddin, Megan Amy. “Systematics and biogeography of Mesobola brevianalis (Boulenger, 1908) (Teleostei: Cyprinidae).” 2015. Web. 05 Mar 2021.

Vancouver:

Riddin MA. Systematics and biogeography of Mesobola brevianalis (Boulenger, 1908) (Teleostei: Cyprinidae). [Internet] [Thesis]. Rhodes University; 2015. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10962/d1017808.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Riddin MA. Systematics and biogeography of Mesobola brevianalis (Boulenger, 1908) (Teleostei: Cyprinidae). [Thesis]. Rhodes University; 2015. Available from: http://hdl.handle.net/10962/d1017808

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

9. Mika, Katelyn Marie. Molecular Evolution of Pregnancy.

Degree: 2018, The University of Chicago

URL: http://pqdtopen.proquest.com/#viewpdf?dispub=10817198

► Unraveling the molecular etiology of a novel phenotype is still a major challenge. Mammalian pregnancy, a novel phenotype, preserves its stepwise evolution in extant… (more)

Subjects/Keywords: Molecular biology; Genetics; Evolution & development

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Mika, K. M. (2018). Molecular Evolution of Pregnancy. (Thesis). The University of Chicago. Retrieved from http://pqdtopen.proquest.com/#viewpdf?dispub=10817198

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Mika, Katelyn Marie. “Molecular Evolution of Pregnancy.” 2018. Thesis, The University of Chicago. Accessed March 05, 2021. http://pqdtopen.proquest.com/#viewpdf?dispub=10817198.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Mika, Katelyn Marie. “Molecular Evolution of Pregnancy.” 2018. Web. 05 Mar 2021.

Vancouver:

Mika KM. Molecular Evolution of Pregnancy. [Internet] [Thesis]. The University of Chicago; 2018. [cited 2021 Mar 05]. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=10817198.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Mika KM. Molecular Evolution of Pregnancy. [Thesis]. The University of Chicago; 2018. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=10817198

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Toronto

10. Rajagopalan, Deepthi. Transcriptome Assembly and Molecular Evolutionary Analysis of Sex-biased Genes in Caenorhabditis Species 9 and Caenorhabditis Species 5.

Degree: 2012, University of Toronto

URL: http://hdl.handle.net/1807/33502

►

Differential gene expression between sexes is the main contributor of the morphological and behavioral differences observed between them. Studying the signatures of these differences at… (more)

Subjects/Keywords: Molecular evolution; Bioinformatics; 0369

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rajagopalan, D. (2012). Transcriptome Assembly and Molecular Evolutionary Analysis of Sex-biased Genes in Caenorhabditis Species 9 and Caenorhabditis Species 5. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/33502

Chicago Manual of Style (16^th Edition):

Rajagopalan, Deepthi. “Transcriptome Assembly and Molecular Evolutionary Analysis of Sex-biased Genes in Caenorhabditis Species 9 and Caenorhabditis Species 5.” 2012. Masters Thesis, University of Toronto. Accessed March 05, 2021. http://hdl.handle.net/1807/33502.

MLA Handbook (7^th Edition):

Rajagopalan, Deepthi. “Transcriptome Assembly and Molecular Evolutionary Analysis of Sex-biased Genes in Caenorhabditis Species 9 and Caenorhabditis Species 5.” 2012. Web. 05 Mar 2021.

Vancouver:

Rajagopalan D. Transcriptome Assembly and Molecular Evolutionary Analysis of Sex-biased Genes in Caenorhabditis Species 9 and Caenorhabditis Species 5. [Internet] [Masters thesis]. University of Toronto; 2012. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1807/33502.

Council of Science Editors:

Rajagopalan D. Transcriptome Assembly and Molecular Evolutionary Analysis of Sex-biased Genes in Caenorhabditis Species 9 and Caenorhabditis Species 5. [Masters Thesis]. University of Toronto; 2012. Available from: http://hdl.handle.net/1807/33502

University of Texas Southwestern Medical Center

11. Salinas, Victor H. Hierarchy of Interactions in Protein Evolution.

Degree: 2016, University of Texas Southwestern Medical Center

URL: http://hdl.handle.net/2152.5/8300

► Deciphering the relationship between genotype and phenotype is complicated by the sheer number of possible cooperative interactions amongst the parts that make up biological systems.… (more)

Subjects/Keywords: Amino Acids; Evolution, Molecular; Proteins

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Salinas, V. H. (2016). Hierarchy of Interactions in Protein Evolution. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/8300

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Salinas, Victor H. “Hierarchy of Interactions in Protein Evolution.” 2016. Thesis, University of Texas Southwestern Medical Center. Accessed March 05, 2021. http://hdl.handle.net/2152.5/8300.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Salinas, Victor H. “Hierarchy of Interactions in Protein Evolution.” 2016. Web. 05 Mar 2021.

Vancouver:

Salinas VH. Hierarchy of Interactions in Protein Evolution. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2016. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2152.5/8300.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Salinas VH. Hierarchy of Interactions in Protein Evolution. [Thesis]. University of Texas Southwestern Medical Center; 2016. Available from: http://hdl.handle.net/2152.5/8300

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of California – San Francisco

12. Nocedal, Isabel. Evolutionary rewiring of the gene regulatory network controlled by Ndt80.

Degree: Biochemistry and Molecular Biology, 2015, University of California – San Francisco

URL: http://www.escholarship.org/uc/item/3gc241r2

► Gene regulatory networks—composed of transcription regulators and their downstream “target” genes—have been shown to control many biological processes, and changes to either the regulators, the… (more)

Subjects/Keywords: Molecular biology; Evolution & development; Genetics

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Nocedal, I. (2015). Evolutionary rewiring of the gene regulatory network controlled by Ndt80. (Thesis). University of California – San Francisco. Retrieved from http://www.escholarship.org/uc/item/3gc241r2

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Nocedal, Isabel. “Evolutionary rewiring of the gene regulatory network controlled by Ndt80.” 2015. Thesis, University of California – San Francisco. Accessed March 05, 2021. http://www.escholarship.org/uc/item/3gc241r2.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Nocedal, Isabel. “Evolutionary rewiring of the gene regulatory network controlled by Ndt80.” 2015. Web. 05 Mar 2021.

Vancouver:

Nocedal I. Evolutionary rewiring of the gene regulatory network controlled by Ndt80. [Internet] [Thesis]. University of California – San Francisco; 2015. [cited 2021 Mar 05]. Available from: http://www.escholarship.org/uc/item/3gc241r2.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Nocedal I. Evolutionary rewiring of the gene regulatory network controlled by Ndt80. [Thesis]. University of California – San Francisco; 2015. Available from: http://www.escholarship.org/uc/item/3gc241r2

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Victoria

13. McRory, John E. Molecular evolution and origin of two peptide superfamilies.

Degree: Department of Biology, 2018, University of Victoria

URL: https://dspace.library.uvic.ca//handle/1828/9715

► In mammals the glucagon and insulin superfamilies each include a number of structurally-related hormones. The origin of each superfamily has been the subject of debate… (more)

▼ In mammals the glucagon and insulin superfamilies each include a number of structurally-related hormones. The origin of each superfamily has been the subject of debate for many years resulting in an hypothesis that each superfamily arose from a single ancestral gene encoding a bioactive molecule. During evolution of the vertebrates, this gene is thought to have duplicated and changed to encode the existing family members. The glucagon superfamily is composed of nine members that have similar intron/exon structure, amino acid sequences and gene length. Two neuropeptides in this family, growth hormone-releasing hormone (GRF) and pituitary adenylate cyclase-activating polypeptide (PACAP) are of special interest in this thesis. In addition to GRF and PACAP, the superfamily is composed of vasoactive intestinal peptide (VIP), peptide histidine methionine (PHM), secretin, glucose-dependent insulin-inducing peptide (GIP), glucagon, and glucagon-like peptide (GLP)-I and -II, This thesis presents nucleotide sequence data from a protochordate (tunicate; Chelysoma productum), bony fish (catfish; Clarias macrocephalus) and bird (chicken; Gallus domesticus) to help in the interpretation of the evolutionary steps in the glucagon superfamily. Molecular biological techniques were used in isolating the grf/pacap cDNA clones from tunicate, catfish and chicken and the genes from tunicate and chicken. It was observed that two family members, GRF and PACAP, are encoded by the same gene in tunicate, catfish and chicken, unlike in mammals where the two peptides are encoded by two separate genes. Therefore, the duplication that gave rise to the two genes must have occurred after the divergence of the reptilian/avian lineage from the mammalian lineage about 250 million years ago. The tunicate, a sister group to amphioxus and the vertebrates, but a taxon that evolved before amphioxus, contains one distinct gene that encodes [special characters omitted] and a second gene encoding [special characters omitted]. These four peptides are short compared to their counterparts in mammals, but the biologically active core is present. The two tunicate cDNA clones have high nucleotide sequence identity (80%) suggesting a recent gene duplication. In addition, a partial gene was isolated for each cDNA. The gene organization shows that [special characters omitted] are each on separate, but adjacent, exons in one gene; likewise [special characters omitted] are on separate exons in the second gene. The degree of identity among the four exons suggests that two tunicate genes resulted from an exon duplication followed by a complete gene duplication. These data suggest that two ancestral tunicate genes are the progenitors from which the existing vertebrate superfamily arose. The evolution of another group of peptides in the insulin superfamily was investigated also. The presence of a distinct insulin and insulin-like growth factor (IGF) within the protochordates (tunicates) was demonstrated using molecular … Advisors/Committee Members: Sherwood, Nancy (supervisor).

Subjects/Keywords: Molecular evolution; Peptide hormones; Glucagon

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

McRory, J. E. (2018). Molecular evolution and origin of two peptide superfamilies. (Thesis). University of Victoria. Retrieved from https://dspace.library.uvic.ca//handle/1828/9715

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

McRory, John E. “Molecular evolution and origin of two peptide superfamilies.” 2018. Thesis, University of Victoria. Accessed March 05, 2021. https://dspace.library.uvic.ca//handle/1828/9715.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

McRory, John E. “Molecular evolution and origin of two peptide superfamilies.” 2018. Web. 05 Mar 2021.

Vancouver:

McRory JE. Molecular evolution and origin of two peptide superfamilies. [Internet] [Thesis]. University of Victoria; 2018. [cited 2021 Mar 05]. Available from: https://dspace.library.uvic.ca//handle/1828/9715.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

McRory JE. Molecular evolution and origin of two peptide superfamilies. [Thesis]. University of Victoria; 2018. Available from: https://dspace.library.uvic.ca//handle/1828/9715

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Louisiana State University

14. McVay, John David. Molecular phylogenetics of the North American snake tribe Thamnophiini.

Degree: PhD, 2013, Louisiana State University

URL: etd-05282013-060302 ; https://digitalcommons.lsu.edu/gradschool_dissertations/1457

► Advancements in phylogenetic theory and methodology coupled with improvements in computational and sequencing technology facilitate study of the divergence and diversification patterns of life. I… (more)

▼ Advancements in phylogenetic theory and methodology coupled with improvements in computational and sequencing technology facilitate study of the divergence and diversification patterns of life. I apply our current understanding to further explore the relationships and evolution of the North American snake tribe Thamnophiini, as well as to address current topics in phylogenetic and taxonomic methodology. There are two paradigms for the phylogenetic analysis of multi-locus sequence data: one which forces all genes to share the same underlying history, and another that allows genes to follow idiosyncratic patterns of descent from ancestral alleles. The first of these approaches (concatenation) is a simplified model of the actual process of genome evolution while the second (species-tree methods) may be overly complex for histories characterized by long divergence times between cladogenesis. Rather than making an a priori determination concerning which of these phylogenetic models to apply to our data, I seek to provide a framework for choosing between concatenation and species-tree methods that treat genes as independently evolving lineages. In Chapter 2 I demonstrate that parametric bootstrapping can be used to assess the extent to which genealogical incongruence across loci can be attributed to phylogenetic estimation error, and demonstrate the application of our approach using an empirical dataset from 10 species of the Natricine snake sub-family. Since our data exhibit incongruence across loci that is clearly caused by a mixture of coalescent stochasticity and phyogenetic estimation error, we also develop an approach for choosing among species tree estimation methods that take gene trees as input and those that simultaneously estimate gene trees and species trees. Ideally, existing taxonomy would be consistent with phylogenetic estimates derived from rigorously analyzed data using appropriate methods. In Chapter 3 I present a multi-locus molecular analysis of the relationships among nine genera in the North American snake tribe Thamnophiini in order to test the monophyly of the crayfish snakes (genus Regina) and the earth snakes (genus Virginia). Sequence data from seven genes were analyzed to assess relationships among representatives of the nine genera by performing multi-locus phylogeny and species tree estimations, and we performed constraint-based tests of monophyly of classic taxonomic designations on a gene-by-gene basis. Estimates of species trees demonstrate that both genera are paraphyletic, and this inference is supported by a concatenated tree. This finding was supported using gene tree constraint tests and Bayes factors, where we rejected the monophyly of both the crayfish snakes (genus Regina) and the earth snakes (genus Virginia). Progress in our understanding of molecular evolution necessitates a more thorough assessment of the phylogeny of thamnophiine snakes, whose relationships have not been fully resolved, and whose previous phylogenetic estimates are based solely on mitochondrial sequence data.…

Subjects/Keywords: evolution; herpetology; molecular systematics

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

McVay, J. D. (2013). Molecular phylogenetics of the North American snake tribe Thamnophiini. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-05282013-060302 ; https://digitalcommons.lsu.edu/gradschool_dissertations/1457

Chicago Manual of Style (16^th Edition):

McVay, John David. “Molecular phylogenetics of the North American snake tribe Thamnophiini.” 2013. Doctoral Dissertation, Louisiana State University. Accessed March 05, 2021. etd-05282013-060302 ; https://digitalcommons.lsu.edu/gradschool_dissertations/1457.

MLA Handbook (7^th Edition):

McVay, John David. “Molecular phylogenetics of the North American snake tribe Thamnophiini.” 2013. Web. 05 Mar 2021.

Vancouver:

McVay JD. Molecular phylogenetics of the North American snake tribe Thamnophiini. [Internet] [Doctoral dissertation]. Louisiana State University; 2013. [cited 2021 Mar 05]. Available from: etd-05282013-060302 ; https://digitalcommons.lsu.edu/gradschool_dissertations/1457.

Council of Science Editors:

McVay JD. Molecular phylogenetics of the North American snake tribe Thamnophiini. [Doctoral Dissertation]. Louisiana State University; 2013. Available from: etd-05282013-060302 ; https://digitalcommons.lsu.edu/gradschool_dissertations/1457

Massey University

15. McComish, Bennet. The covarion model of molecular evolution.

Degree: M. Phil., Biology, 1997, Massey University

URL: http://hdl.handle.net/10179/12364

► Current methods for constructing evolutionary trees generally do not work well for sequences in which multiple substitutions have occurred. The covarion hypothesis may provide a… (more)

Subjects/Keywords: Molecular evolution

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

McComish, B. (1997). The covarion model of molecular evolution. (Masters Thesis). Massey University. Retrieved from http://hdl.handle.net/10179/12364

Chicago Manual of Style (16^th Edition):

McComish, Bennet. “The covarion model of molecular evolution.” 1997. Masters Thesis, Massey University. Accessed March 05, 2021. http://hdl.handle.net/10179/12364.

MLA Handbook (7^th Edition):

McComish, Bennet. “The covarion model of molecular evolution.” 1997. Web. 05 Mar 2021.

Vancouver:

McComish B. The covarion model of molecular evolution. [Internet] [Masters thesis]. Massey University; 1997. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10179/12364.

Council of Science Editors:

McComish B. The covarion model of molecular evolution. [Masters Thesis]. Massey University; 1997. Available from: http://hdl.handle.net/10179/12364

Massey University

16. Yulo, Paul Richard Jesena. Evolution of the spherical cell shape in bacteria.

Degree: PhD, Genetics, 2019, Massey University

URL: http://hdl.handle.net/10179/15503

► Cell shape is an important feature of bacterial cells. It is involved in critical aspects of bacterial cell biology such as motility, growth, and the… (more)

Subjects/Keywords: Bacteria; Morphology; Evolution; Molecular microbiology

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Yulo, P. R. J. (2019). Evolution of the spherical cell shape in bacteria. (Doctoral Dissertation). Massey University. Retrieved from http://hdl.handle.net/10179/15503

Chicago Manual of Style (16^th Edition):

Yulo, Paul Richard Jesena. “Evolution of the spherical cell shape in bacteria.” 2019. Doctoral Dissertation, Massey University. Accessed March 05, 2021. http://hdl.handle.net/10179/15503.

MLA Handbook (7^th Edition):

Yulo, Paul Richard Jesena. “Evolution of the spherical cell shape in bacteria.” 2019. Web. 05 Mar 2021.

Vancouver:

Yulo PRJ. Evolution of the spherical cell shape in bacteria. [Internet] [Doctoral dissertation]. Massey University; 2019. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10179/15503.

Council of Science Editors:

Yulo PRJ. Evolution of the spherical cell shape in bacteria. [Doctoral Dissertation]. Massey University; 2019. Available from: http://hdl.handle.net/10179/15503

University of Sydney

17. Tong, Kwei Jun. Investigating Evolutionary History Using Phylogenomics .

Degree: 2018, University of Sydney

URL: http://hdl.handle.net/2123/17979

► Reconstructing the Tree of Life is one of the principal aims of evolutionary biology. The development of molecular phylogenetics to elucidate evolutionary history has complemented… (more)

▼ Reconstructing the Tree of Life is one of the principal aims of evolutionary biology. The development of molecular phylogenetics to elucidate evolutionary history has complemented palaeontology, biogeography, and archaeology in elucidating biological history. The development of molecular-clock analyses allowed evolutionary timescales to be estimated using nucleotide sequences and other products of the evolutionary process Until recently, the twin challenges of molecular dating were in obtaining sufficient data and developing robust methods. The former concern is now less important as high–throughput sequencing technology allows entire genomes to be sampled. Genome–scale data enhances statistical power, but accompanying this wealth of data is a new suite of analytical challenges. One of these key challenges is analysing these data in synthesis with the paleontological record without statistical overparameterisation. There are also aspects of the evolutionary process, such as among–lineage rate variation, that can affect the precision and accuracy of current methods. In this thesis, I first use the richest nucleotide sequence data set of insects available to estimate an authoritative insect evolutionary timescale that dates the origins and diversification of every major insect order. I then focus on molecular-clock methods by testing their performance in inferring evolutionary rates from time–structured data, common in the study of ancient DNA. I find that among–rate lineage variation and phylo–temporal clustering affect rate estimates. I also study data partitioning, a common technique used to optimise the analysis of multilocus data where independent parameters are applied across different subsets of the data. New data from the genomic revolution gifts biologists new opportunities to re-examine enduring questions about the evolutionary process. Here, I use phylogenetic tools to show that evolution leaves figurative fingerprints on genomes over millions of years.

Subjects/Keywords: evolution; phylogenetics; molecular clock; genomics

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Tong, K. J. (2018). Investigating Evolutionary History Using Phylogenomics . (Thesis). University of Sydney. Retrieved from http://hdl.handle.net/2123/17979

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Tong, Kwei Jun. “Investigating Evolutionary History Using Phylogenomics .” 2018. Thesis, University of Sydney. Accessed March 05, 2021. http://hdl.handle.net/2123/17979.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Tong, Kwei Jun. “Investigating Evolutionary History Using Phylogenomics .” 2018. Web. 05 Mar 2021.

Vancouver:

Tong KJ. Investigating Evolutionary History Using Phylogenomics . [Internet] [Thesis]. University of Sydney; 2018. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2123/17979.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tong KJ. Investigating Evolutionary History Using Phylogenomics . [Thesis]. University of Sydney; 2018. Available from: http://hdl.handle.net/2123/17979

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas – Austin

18. Liebeskind, Benjamin Joseph. Ion channels and the tree of life.

Degree: PhD, Ecology, Evolution and Behavior, 2014, University of Texas – Austin

URL: http://hdl.handle.net/2152/44128

► The field of comparative neurobiology has deep roots. I will begin by giving an overview of the parts of its history that I feel are… (more)

▼ The field of comparative neurobiology has deep roots. I will begin by giving an overview of the parts of its history that I feel are most relevant for this dissertation. Within this history lies a wealth of zoological research and penetrating theories that are underutilized by modern evolutionary biologists. The age of whole-genome sequencing provides a perfect opportunity to revisit and perhaps update this corpus to better understand the phylogenetic history of organismal behavior. The first three chapters of my dissertation will be case studies on the evolution of sodium-selective ion channels. Sodium channels are responsible for much of the electrical signaling in animal nervous systems and muscles, but their evolutionary relationships have not yet been explored with the modern tools of phylogenetics and comparative genomics. Chapter 1 will deal with the classic Nav channels which create action potentials in nerves and muscles. There I will show that this gene family pre-dates the nervous system and even animal multicellularity. Chapter two will investigate sodium leak channels, which likley create the leak conductance measured by Hodgkin and Huxley. These channels turn out to be close relatives of fungal calcium channels, a relationship which illuminates the evolution of both groups. Chapter three is on bacterial sodium channels and their use as models for other sodium channel types. The final chapter will turn away from sodium channels in particular and discuss the evolution of animal nervous systems by means of ion channel genomics. In that chapter I will show that the genomic complements of ion channels that animals with nervous systems possess evolved independently to large degree, and that the early evolution of nervous systems also involved periods of gene loss. I will end with a more general discussion of convergent evolution, a key theme of this dissertation, and its effect on comparative analyses in the age of genomics. Advisors/Committee Members: Zakon, H. H. (advisor), Hillis, David M., 1958- (advisor), Aldrich, Richard W (committee member), Hofmann, Hans A (committee member), Matz, Mikhail V (committee member).

Subjects/Keywords: Sodium channel; Molecular evolution

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Liebeskind, B. J. (2014). Ion channels and the tree of life. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/44128

Chicago Manual of Style (16^th Edition):

Liebeskind, Benjamin Joseph. “Ion channels and the tree of life.” 2014. Doctoral Dissertation, University of Texas – Austin. Accessed March 05, 2021. http://hdl.handle.net/2152/44128.

MLA Handbook (7^th Edition):

Liebeskind, Benjamin Joseph. “Ion channels and the tree of life.” 2014. Web. 05 Mar 2021.

Vancouver:

Liebeskind BJ. Ion channels and the tree of life. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2014. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2152/44128.

Council of Science Editors:

Liebeskind BJ. Ion channels and the tree of life. [Doctoral Dissertation]. University of Texas – Austin; 2014. Available from: http://hdl.handle.net/2152/44128

19. Kavalco, Karine Frehner. Estudos evolutivos no gênero Astyanax (Pisces, Characidae).

Degree: PhD, Biologia (Genética), 2008, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/41/41131/tde-29102008-174719/ ;

►

O gênero Astyanax é um dos mais especiosos da ordem Characiformes. Suas mais de 100 espécies distribuemse por praticamente toda a região Neotropical e habitam… (more)

▼

O gênero Astyanax é um dos mais especiosos da ordem Characiformes. Suas mais de 100 espécies distribuemse por praticamente toda a região Neotropical e habitam os mais diversos ambientes, como regiões montanhosas, trechos lóticos e leitos de rios, porções lênticas ou lagunares e nascentes. Durante cerca de trinta anos estes peixes têm sido alvo de estudos cromossômicos, que os caracterizaram como um grupo com grande diversidade citogenética. Recentemente, o advento de técnicas de citogenética molecular e de estudos empregando marcadores de DNA tem produzido novos dados sobre a biologia evolutiva do grupo, e possibilitado a revisitação de antigos problemas do gênero, como sua difícil classificação taxonômica. No presente trabalho buscouse a caracterização citogenética e a análise de segmentos do mtDNA (seqüências parciais das regiões dos genes ND2 e ATPase6/8) de diferentes espécies e populações de Astyanax, com a finalidade de contribuir para o reconhecimento de padrões e processos evolutivos no gênero. Foram analisados exemplares provenientes das bacias hidrográficas dos rios São Francisco, Tietê, Paranapanema, MogiGuaçu, Iguaçu, Paraíba do Sul, Ribeira de Iguape e Guapimirim. Os resultados forneceram panoramas filogeográficos e estabeleceram relações evolutivas entre as espécies analisadas, utilizando dados associados de duas classes diferentes de marcadores genéticos. Através da aplicação de técnicas citogenéticas clássicas e moleculares são apresentados dados cariotípicos de A. altiparanae, A. aff. bimaculatus, A. bockmanni, A. aff. fasciatus, A. hastatus, A. mexicanus e A. ribeirae. Nos estudos filogenéticos foram utilizadas, adicionalmente às seqüências das espécies acima citadas, dados provenientes de Astyanax sp.B, A. giton, A. intermedius, A. lacustris, A. aff. scabripinnis, Bryconamericus iheringii, Mimagoniatis microlepis e Roeboides occidentalis. Foram ainda incluídas nas análises seqüências do mtDNA de haplótipos diferentes de A. mexicanus e A. bimaculatus retirados da literatura. Para as diferentes populações amostradas dos grupos A. altiparanae, A. aff. bimaculatus e A. aff. fasciatus, foram efetuadas análises filogeográficas associadas a dados cromossômicos. As análises cromossômicas e moleculares do sistema de drenagem do Leste e de bacias circunvizinhas apresentadas no presente trabalho forneceram dados adicionais para o entendimento da biologia evolutiva do gênero Astyanax. iv Outra contribuição do presente estudo foi a inferência das relações evolutivas de algumas das mais bem estudadas espécies do gênero Astyanax, que a despeito da sua importância ecológica e de constituírem um modelo para estudos cromossômicos e evolutivos, ainda não apresentam estudos filogenéticos amplos. Ainda, a associação de dados cromossômicos e moleculares forneceu um panorama interessante sobre as relações evolutivas em algumas espécies do gênero, bem como sobre os processos e padrões evolutivos presentes nos Astyanax.

Astyanax is one of the species-richest genera within the order Characiformes. More than 100…

Advisors/Committee Members: Toledo, Lurdes Foresti de Almeida.

Subjects/Keywords: Astyanax; Astyanax; Evolução Cariotípica; Evolução Molecular; Karyotypic evolution; Molecular evolution.

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kavalco, K. F. (2008). Estudos evolutivos no gênero Astyanax (Pisces, Characidae). (Doctoral Dissertation). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/41/41131/tde-29102008-174719/ ;

Chicago Manual of Style (16^th Edition):

Kavalco, Karine Frehner. “Estudos evolutivos no gênero Astyanax (Pisces, Characidae).” 2008. Doctoral Dissertation, University of São Paulo. Accessed March 05, 2021. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-29102008-174719/ ;.

MLA Handbook (7^th Edition):

Kavalco, Karine Frehner. “Estudos evolutivos no gênero Astyanax (Pisces, Characidae).” 2008. Web. 05 Mar 2021.

Vancouver:

Kavalco KF. Estudos evolutivos no gênero Astyanax (Pisces, Characidae). [Internet] [Doctoral dissertation]. University of São Paulo; 2008. [cited 2021 Mar 05]. Available from: http://www.teses.usp.br/teses/disponiveis/41/41131/tde-29102008-174719/ ;.

Council of Science Editors:

Kavalco KF. Estudos evolutivos no gênero Astyanax (Pisces, Characidae). [Doctoral Dissertation]. University of São Paulo; 2008. Available from: http://www.teses.usp.br/teses/disponiveis/41/41131/tde-29102008-174719/ ;

University of Colorado

20. Turk, Rebecca Marie. Small RNA-amino acid interactions and implications for the origin of translation.

Degree: PhD, Biology, 2010, University of Colorado

URL: https://scholar.colorado.edu/mcdb_gradetds/4

► Ribonucleic acid (RNA) has the ability to store and transfer genetic information, and also to catalyze chemical reactions. This observation has led to the… (more)

▼ Ribonucleic acid (RNA) has the ability to store and transfer genetic information, and also to catalyze chemical reactions. This observation has led to the RNA world hypothesis, which states that there was likely a time in early evolution (before DNA and proteins) in which RNA carried out both these functions. In particular, RNA may have played an important role in the origin of protein (peptide) synthesis, or translation. While modern protein synthesis requires protein catalysis or stabilization at each of the relevant chemical steps, RNA is the functional heart of the ribosome. There must have been a mechanism in place to synthesize the first proteins, which logically could not have been protein-catalyzed. Early proteins, then, may have been synthesized by RNA catalysts. Most previously characterized RNA enzymes, or ribozymes, are relatively complex. This makes their existence in the early RNA world problematic, since even RNA synthesis must have been relatively inefficient. In this work, I show that a ribozyme that is only five nucleotides long can catalyze one of the reactions relevant to protein synthesis, aminoacylation of an RNA substrate, using the same reactants that biology uses today. In addition, this ribozyme/substrate complex hosts the formation of RNA-peptides and aminoacyl- and peptidyl-RNA diesters. In addition, no ribozymes have been found which catalyze the final crucial step of protein synthesis, peptide bond formation. I approach this problem by showing that RNAs that bind specifically to a dipeptide can be derived through in vitro selection. Therefore, RNAs can bind to two amino acids simultaneously. This observation strengthens the argument that the first peptides could have formed from specific, direct interactions between amino acids and RNA. The conclusion of this work is that small RNAs may have served important functions in the origin of translation during the RNA world. The formation of an ester bond between an amino acid and an RNA molecule can be catalyzed by RNA with very little sequence information. Moreover, I show that the RNA can interact specifically not just with individual amino acids, but also with multiple amino acids. This may provide an explanation for how the first coded peptides formed in the absence of protein catalysts. Advisors/Committee Members: Michael Yarus, Norman Pace, Rob Knight.

Subjects/Keywords: aptamer; evolution; ribozyme; RNA; translation; Evolution; Molecular Biology; Molecular Genetics

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Turk, R. M. (2010). Small RNA-amino acid interactions and implications for the origin of translation. (Doctoral Dissertation). University of Colorado. Retrieved from https://scholar.colorado.edu/mcdb_gradetds/4

Chicago Manual of Style (16^th Edition):

Turk, Rebecca Marie. “Small RNA-amino acid interactions and implications for the origin of translation.” 2010. Doctoral Dissertation, University of Colorado. Accessed March 05, 2021. https://scholar.colorado.edu/mcdb_gradetds/4.

MLA Handbook (7^th Edition):

Turk, Rebecca Marie. “Small RNA-amino acid interactions and implications for the origin of translation.” 2010. Web. 05 Mar 2021.

Vancouver:

Turk RM. Small RNA-amino acid interactions and implications for the origin of translation. [Internet] [Doctoral dissertation]. University of Colorado; 2010. [cited 2021 Mar 05]. Available from: https://scholar.colorado.edu/mcdb_gradetds/4.

Council of Science Editors:

Turk RM. Small RNA-amino acid interactions and implications for the origin of translation. [Doctoral Dissertation]. University of Colorado; 2010. Available from: https://scholar.colorado.edu/mcdb_gradetds/4

University of Washington

21. Kursel, Lisa Elaine. Gametic specialization of centromeric histone paralogs in insect species.

Degree: PhD, 2019, University of Washington

URL: http://hdl.handle.net/1773/43425

► The centromere is a specialized chromatin region that is critical for faithful chromosome segregation. Centromere function is conferred epigenetically, by the presence of a histone… (more)

Subjects/Keywords: CenH3; Centromere; Drosophila; Molecular evolution; Positive selection; Molecular biology; Evolution & development; Molecular and cellular biology

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kursel, L. E. (2019). Gametic specialization of centromeric histone paralogs in insect species. (Doctoral Dissertation). University of Washington. Retrieved from http://hdl.handle.net/1773/43425

Chicago Manual of Style (16^th Edition):

Kursel, Lisa Elaine. “Gametic specialization of centromeric histone paralogs in insect species.” 2019. Doctoral Dissertation, University of Washington. Accessed March 05, 2021. http://hdl.handle.net/1773/43425.

MLA Handbook (7^th Edition):

Kursel, Lisa Elaine. “Gametic specialization of centromeric histone paralogs in insect species.” 2019. Web. 05 Mar 2021.

Vancouver:

Kursel LE. Gametic specialization of centromeric histone paralogs in insect species. [Internet] [Doctoral dissertation]. University of Washington; 2019. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1773/43425.

Council of Science Editors:

Kursel LE. Gametic specialization of centromeric histone paralogs in insect species. [Doctoral Dissertation]. University of Washington; 2019. Available from: http://hdl.handle.net/1773/43425

University of California – Irvine

22. Ravikumar, Arjun. An orthogonal DNA replication system for in vivo continuous directed evolution.

Degree: Biomedical Engineering, 2018, University of California – Irvine

URL: http://www.escholarship.org/uc/item/78b901hc

► Directed evolution is a powerful approach for engineering biomolecules and understanding the basic principles of adaptation. However, experimental strategies for directed evolution are notoriously labor-intensive… (more)

Subjects/Keywords: Bioengineering; Molecular biology; biomolecular evolution; continuous evolution; directed evolution; drug resistance; error threshold; orthogonal replication

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ravikumar, A. (2018). An orthogonal DNA replication system for in vivo continuous directed evolution. (Thesis). University of California – Irvine. Retrieved from http://www.escholarship.org/uc/item/78b901hc

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ravikumar, Arjun. “An orthogonal DNA replication system for in vivo continuous directed evolution.” 2018. Thesis, University of California – Irvine. Accessed March 05, 2021. http://www.escholarship.org/uc/item/78b901hc.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ravikumar, Arjun. “An orthogonal DNA replication system for in vivo continuous directed evolution.” 2018. Web. 05 Mar 2021.

Vancouver:

Ravikumar A. An orthogonal DNA replication system for in vivo continuous directed evolution. [Internet] [Thesis]. University of California – Irvine; 2018. [cited 2021 Mar 05]. Available from: http://www.escholarship.org/uc/item/78b901hc.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ravikumar A. An orthogonal DNA replication system for in vivo continuous directed evolution. [Thesis]. University of California – Irvine; 2018. Available from: http://www.escholarship.org/uc/item/78b901hc

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universiteit Utrecht

23. Kruse, F.K. Regeneration and the underlying mechanisms.

Degree: 2012, Universiteit Utrecht

URL: http://dspace.library.uu.nl:8080/handle/1874/253567

► Regeneration is generally defined as tissue replacement after pathological insult such as injury or disease. It has captured the attention of many biologists, clinicians and… (more)

Subjects/Keywords: Regeneration; Stem cells; Evolution; Molecular mechanisms; Metazoan

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kruse, F. K. (2012). Regeneration and the underlying mechanisms. (Masters Thesis). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/253567

Chicago Manual of Style (16^th Edition):

Kruse, F K. “Regeneration and the underlying mechanisms.” 2012. Masters Thesis, Universiteit Utrecht. Accessed March 05, 2021. http://dspace.library.uu.nl:8080/handle/1874/253567.

MLA Handbook (7^th Edition):

Kruse, F K. “Regeneration and the underlying mechanisms.” 2012. Web. 05 Mar 2021.

Vancouver:

Kruse FK. Regeneration and the underlying mechanisms. [Internet] [Masters thesis]. Universiteit Utrecht; 2012. [cited 2021 Mar 05]. Available from: http://dspace.library.uu.nl:8080/handle/1874/253567.

Council of Science Editors:

Kruse FK. Regeneration and the underlying mechanisms. [Masters Thesis]. Universiteit Utrecht; 2012. Available from: http://dspace.library.uu.nl:8080/handle/1874/253567

Iowa State University

24. Kayal, Ehsan. The evolution of the mitochondrial genomes of calcareous sponges and cnidarians.

Degree: 2012, Iowa State University

URL: http://pqdtopen.proquest.com/#viewpdf?dispub=3539503

► The mitochondrial DNA (mtDNA) in animals (Metazoa) is a favorite molecule for phylogenetic studies given its relative uniformity in both size and organization. Yet,… (more)

▼ The mitochondrial DNA (mtDNA) in animals (Metazoa) is a favorite molecule for phylogenetic studies given its relative uniformity in both size and organization. Yet, as the depth coverage of representative animal groups increases sharply thanks to recent advances in sequencing technology, some clades remain stubbornly under sampled, if even represented at all. Difficulties associated with data collection from problematic taxa can arise from highly derived sequences, fragmented genomes, unusual structure, or any combination of these. Particularly illustrative examples are found in non-bilaterian animals (placozoans, sponges, cnidarians, comb jellies) where the mtDNA is more variable in size and structure. The present dissertation provides several case studies of what is considered “unusual” mtDNA for animals. First, we describe some unusual characteristics of the mitochondrial genomes found in calcareous sponges (Calcarea, Porifera), where one, potentially two, novel genetic codes are inferred, transfer RNAs (tRNAs) are edited, and ribosomal RNA (rRNA) genes are in pieces. We also hypothesize that the mtDNA is linear and multipartite. Then, we explore the evolution of the mtDNA in medusozoan cnidarians (Medusozoa, Cnidaria). The mtDNA in Medusozoa is linear, and encodes two extra protein genes (lost in one clade) putatively involved in the maintenance and replication of the linear chromosomes. In addition, secondary segmentalization has occurred independently in some hydras (Hydridae) and box jellies (Cubozoa). Using the sequences from these mito-genomes, we propose a new phylogeny for Cnidaria, providing additional support for the clade [Medusozoa + Octocorallia], rendering Anthozoa (Hexacorallia + Octocorallia) paraphyletic. Finally, this dissertation concludes by a mini review stating the current state of knowledge of metazoan mtDNA and some of the pitfalls in the field of mitogenomics. In particular, the new findings further challenge the classical idea of a uniform mtDNA organization (frozen genome) in animals, and question any directional explanation of the evolution of the mtDNA in animals.

Subjects/Keywords: Biology, Molecular; Biology, Evolution and Development

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kayal, E. (2012). The evolution of the mitochondrial genomes of calcareous sponges and cnidarians. (Thesis). Iowa State University. Retrieved from http://pqdtopen.proquest.com/#viewpdf?dispub=3539503

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Kayal, Ehsan. “The evolution of the mitochondrial genomes of calcareous sponges and cnidarians.” 2012. Thesis, Iowa State University. Accessed March 05, 2021. http://pqdtopen.proquest.com/#viewpdf?dispub=3539503.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Kayal, Ehsan. “The evolution of the mitochondrial genomes of calcareous sponges and cnidarians.” 2012. Web. 05 Mar 2021.

Vancouver:

Kayal E. The evolution of the mitochondrial genomes of calcareous sponges and cnidarians. [Internet] [Thesis]. Iowa State University; 2012. [cited 2021 Mar 05]. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=3539503.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Kayal E. The evolution of the mitochondrial genomes of calcareous sponges and cnidarians. [Thesis]. Iowa State University; 2012. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=3539503

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

The University of Iowa

25. Pightling, Arthur William. The evolutionary history of meiotic genes| Early origins by duplication and subsequent losses.

Degree: 2012, The University of Iowa

URL: http://pqdtopen.proquest.com/#viewpdf?dispub=3516665

► Meiosis is necessary for sexual reproduction in eukaryotes. Genetic recombination between non-sister homologous chromosomes is needed in most organisms for successful completion of the… (more)

▼ Meiosis is necessary for sexual reproduction in eukaryotes. Genetic recombination between non-sister homologous chromosomes is needed in most organisms for successful completion of the first meiotic division. Proteins that function during meiotic recombination have been studied extensively in model organisms. However, less is known about the evolution of these proteins, especially among protists. We searched the genomes of diverse eukaryotes, representing all currently recognized supergroups, for 26 genes encoding proteins important for different stages of interhomolog recombination. We also performed phylogenetic analyses to determine the evolutionary relationships of gene homologs. At least 23 of the genes tested (nine that are known to function only during meiosis in model organisms) are likely to have been present in the Last Eukaryotic Common Ancestor (LECA). These genes encode products that function during: (i) synaptonemal complex formation; (ii) interhomolog DNA strand exchange; (iii) Holliday junction resolution; and (iv) sister-chromatid cohesion. These data strongly suggest that the LECA was capable of these distinct and important functions during meiosis. We also determined that several genes whose products function during both mitosis and meiosis are paralogs of genes whose products are known to function only during meiosis. Therefore, these meiotic genes likely arose by duplication events that occurred prior to the LECA. The Rad51 protein catalyzes DNA strand exchange during both mitosis and meiosis, while Dmc1 catalyzes interhomolog DNA strand exchange only during meiosis. To study the evolution of these important proteins, we performed degenerate PCR and extensive nucleotide and protein sequence database searches to obtain data from representatives of all available eukaryotic supergroups. We also performed phylogenetic analyses on the Rad51 and Dmc1 protein sequence data obtained to evaluate their utility as phylogenetic markers. We determined that evolutionary relationships of five of the six currently recognized eukaryotic supergroups are supported with Bayesian phylogenetic analyses. Using this dataset, we also identified ten amino acid residues that are highly conserved among Rad51 and Dmc1 protein sequences and, therefore, are likely to confer protein-specific functions. Due to the distributions of these residues, they are likely to have been present in the Rad51 and Dmc1 proteins of the LECA. To address an important issue with the gene inventory method of scientific inquiry, we developed a heuristic metric for determining whether apparent gene absences are due to limitations of the sequence search regimen or represent true losses of genes from genomes. We collected RNA polymerase I (Pol I), Replication Protein A (RPA), and DNA strand exchange (SE) sequence data from 47 diverse eukaryotes. We then compared the numbers of apparent absences to a single measure of protein sequence length and sequence conservation (Smith-Waterman pairwise alignment (S-W) scores) obtained by…

Subjects/Keywords: Biology, Molecular; Biology, Evolution and Development

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Pightling, A. W. (2012). The evolutionary history of meiotic genes| Early origins by duplication and subsequent losses. (Thesis). The University of Iowa. Retrieved from http://pqdtopen.proquest.com/#viewpdf?dispub=3516665

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Pightling, Arthur William. “The evolutionary history of meiotic genes| Early origins by duplication and subsequent losses.” 2012. Thesis, The University of Iowa. Accessed March 05, 2021. http://pqdtopen.proquest.com/#viewpdf?dispub=3516665.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Pightling, Arthur William. “The evolutionary history of meiotic genes| Early origins by duplication and subsequent losses.” 2012. Web. 05 Mar 2021.

Vancouver:

Pightling AW. The evolutionary history of meiotic genes| Early origins by duplication and subsequent losses. [Internet] [Thesis]. The University of Iowa; 2012. [cited 2021 Mar 05]. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=3516665.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Pightling AW. The evolutionary history of meiotic genes| Early origins by duplication and subsequent losses. [Thesis]. The University of Iowa; 2012. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=3516665

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

UCLA

26. Macadangdang, Benjamin. The Evolutionary Roles of H2A and H2B in Genome Compaction in Eukaryotes.

Degree: Molecular Biology, 2014, UCLA

URL: http://www.escholarship.org/uc/item/7jh207mn

► As eukaryotes have evolved from simple, unicellular organisms to more complex multicellular species, both the genome size and the nuclear volume have increased. However, the… (more)

▼ As eukaryotes have evolved from simple, unicellular organisms to more complex multicellular species, both the genome size and the nuclear volume have increased. However, the rates of increase of these two parameters have not been equal with genome size increasing much faster than the volume of the nucleus. This disproportionality has necessitated an increase in chromatin compaction for larger genome organisms. Although histones, through formation of the nucleosome, are the basic building blocks of chromatin, it is unknown whether histones have evolved to facilitate these higher compaction ratios. Analysis of histone sequences from 160 organisms representing all eukaryotic kingdoms revealed that there are significant changes in both the H2A N-terminus and H2B C-terminus sequences that have systematically evolved as genomes expanded. In the H2A N-terminus, larger genome species have acquired more arginines, and in the H2B C-terminus, lysines. In parallel with acquisition of positively charged residues, both H2A and H2B have lost polar residues. To determine whether these evolutionary sequence changes contribute to increased genome compaction, a series of in vivo and in vitro molecular biological and biochemical experiments were carried out using both budding yeast and human cell lines as model systems. Insertion of precisely positioned arginines into the H2A N-terminus of a small-genome organism substantially increased chromatin compaction while their absence markedly diminished compaction in cells with large genomes. This effect was recapitulated using in vitro assembled nucleosomal arrays with unmodified histones, indicating that H2A N-terminus directly modulates the chromatin fiber likely through intra- and inter-nucleosomal arginine-DNA contacts to enable tighter compaction. Insertions of lysines into the H2B C-terminus of a small genome organism also increased compaction. Combinations of H2A-H2B sequence changes revealed that chromatin compaction is enhanced as compared to single histone mediated compaction and that the H2A N-terminus and H2B C-terminus work additively. An area physically near the H2B C-terminus in the nucleosomal structure, which I have termed the ABC Domain (H2A/H2B Compaction Domain), accounts for the majority of the chromatin compaction mediated by H2A and H2B. These findings reveal a simple evolutionary mechanism for regulation of chromatin compaction that has enabled organisms with larger genome achieve higher compaction ratios.

Subjects/Keywords: Molecular biology; Chromatin; Compaction; Eukaryote; Evolution; Histones

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Macadangdang, B. (2014). The Evolutionary Roles of H2A and H2B in Genome Compaction in Eukaryotes. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/7jh207mn

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Macadangdang, Benjamin. “The Evolutionary Roles of H2A and H2B in Genome Compaction in Eukaryotes.” 2014. Thesis, UCLA. Accessed March 05, 2021. http://www.escholarship.org/uc/item/7jh207mn.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Macadangdang, Benjamin. “The Evolutionary Roles of H2A and H2B in Genome Compaction in Eukaryotes.” 2014. Web. 05 Mar 2021.

Vancouver:

Macadangdang B. The Evolutionary Roles of H2A and H2B in Genome Compaction in Eukaryotes. [Internet] [Thesis]. UCLA; 2014. [cited 2021 Mar 05]. Available from: http://www.escholarship.org/uc/item/7jh207mn.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Macadangdang B. The Evolutionary Roles of H2A and H2B in Genome Compaction in Eukaryotes. [Thesis]. UCLA; 2014. Available from: http://www.escholarship.org/uc/item/7jh207mn

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of California – Berkeley

27. Abedin, Monika. Cadherin evolution and the origin of animals.

Degree: Molecular & Cell Biology, 2010, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/59s8x1cb

► The question of how animals evolved from a unicellular ancestor has challenged evolutionary biologists for decades. Because cell adhesion and signaling are required for multicellularity,… (more)

▼ The question of how animals evolved from a unicellular ancestor has challenged evolutionary biologists for decades. Because cell adhesion and signaling are required for multicellularity, understanding how these cellular processes evolved will provide key insights into the origin of animals. A critical finding is that choanoflagellates, the closest living unicellular relatives of animals, express members of the cadherin superfamily. Cadherins are pivotal for animal cell adhesion and signaling and were previously thought to be unique to animals, making them crucial to understanding the evolutionary origin and transition to multicellularity. Importantly, the presence of cadherins in choanoflagellates allows a consideration of their ancestral function in the unicellular progenitor of animals. To gain insight into the ancestral structure and function of cadherins, I reconstructed the domain content of cadherins from the last common ancestor of choanoflagellates and metazoans. Conservation of diverse protein domains in the choanoflagellate Monosiga brevicollis and metazoan cadherins suggests that ancestral cadherins served both signaling and adhesive functions. I find that two M. brevicollis cadherin containing an ancestral domain combination MBCDH1 and a close paralog, MBCDH2, localize to the actin-filled microvilli of the feeding collar. Interestingly, the protein abundance of these cadherins changes in response to bacterial food availability. In vitro studies, as well as experiments performed in a heterologous cell culture system, suggest that MBCDH1 does not mediate homophilic adhesion in the context of these experiments like some metazoan cadherins and thus may play a role in cell signaling. Taken together, these data suggest that cadherins may mediate interactions with the extracellular environment, including the recognition and capture of bacterial prey. I hypothesize that metazoan cadherins were co-opted to mediate cell-cell interactions from ancestral proteins that interpreted and responded to extracellular cues.

Subjects/Keywords: Evolution and Development; Biology, Molecular; Biology, Cell

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Abedin, M. (2010). Cadherin evolution and the origin of animals. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/59s8x1cb

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Abedin, Monika. “Cadherin evolution and the origin of animals.” 2010. Thesis, University of California – Berkeley. Accessed March 05, 2021. http://www.escholarship.org/uc/item/59s8x1cb.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Abedin, Monika. “Cadherin evolution and the origin of animals.” 2010. Web. 05 Mar 2021.

Vancouver:

Abedin M. Cadherin evolution and the origin of animals. [Internet] [Thesis]. University of California – Berkeley; 2010. [cited 2021 Mar 05]. Available from: http://www.escholarship.org/uc/item/59s8x1cb.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Abedin M. Cadherin evolution and the origin of animals. [Thesis]. University of California – Berkeley; 2010. Available from: http://www.escholarship.org/uc/item/59s8x1cb

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Michigan

28. Bakewell, Margaret A. Genomic Patterns of Gene Evolution.

Degree: PhD, Ecology and Evolutionary Biology, 2011, University of Michigan

URL: http://hdl.handle.net/2027.42/86280

► The bounty of genomic sequence and supporting genomic datasets such as expression data enables study of the genomic patterns of gene evolution. Such studies can… (more)

Subjects/Keywords: Molecular Evolution; Ecology and Evolutionary Biology; Science

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Bakewell, M. A. (2011). Genomic Patterns of Gene Evolution. (Doctoral Dissertation). University of Michigan. Retrieved from http://hdl.handle.net/2027.42/86280

Chicago Manual of Style (16^th Edition):

Bakewell, Margaret A. “Genomic Patterns of Gene Evolution.” 2011. Doctoral Dissertation, University of Michigan. Accessed March 05, 2021. http://hdl.handle.net/2027.42/86280.

MLA Handbook (7^th Edition):

Bakewell, Margaret A. “Genomic Patterns of Gene Evolution.” 2011. Web. 05 Mar 2021.

Vancouver:

Bakewell MA. Genomic Patterns of Gene Evolution. [Internet] [Doctoral dissertation]. University of Michigan; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2027.42/86280.

Council of Science Editors:

Bakewell MA. Genomic Patterns of Gene Evolution. [Doctoral Dissertation]. University of Michigan; 2011. Available from: http://hdl.handle.net/2027.42/86280

Cornell University

29. Savage, Anna. Immunogenetic Adaptation To An Emergent Amphibian Disease.

Degree: PhD, Ecology, 2012, Cornell University

URL: http://hdl.handle.net/1813/29197

► The disease chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), emerged in the 1970s and has caused the decline and extinction of hundreds of… (more)

▼ The disease chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), emerged in the 1970s and has caused the decline and extinction of hundreds of amphibian species worldwide. Several pathogen and environmental factors have been identified that play critical roles in determining Bd disease dynamics. In comparison, host factors have been infrequently characterized and remain poorly understood. Here, I explore genetic responses to Bd in the lowland leopard frog (Lithobates yavapaiensis) to evaluate the hypothesis that host genetic factors contribute to Bd susceptibility across natural populations. I characterize disease prevalence, environmental variables, and measures of genetic variability in eleven natural populations to reveal spatial and temporal Bd dynamics. I also perform experimental Bd infections in lab-reared frogs collected from five natural populations. For both experimentally reared frogs and natural populations, I characterize allelic variation at an expressed Major Histocompatibility Complex (MHC) class IIB locus that encodes peptides that initiate acquired immunity. I find that infections are minimal in summer but abundant in winter, some populations are Bd infected without developing chytridiomycosis, and other populations are Bd infected and experience fatal bouts of chytridiomycosis. I identify an outlier locus that shows associations to Bd susceptibility, and find the best models predicting Bd dynamics include both genetic diversity and environmental variables. I show that MHC alleles associate with surviving Bd infection in both lab-infected frogs and naturally sampled iv individuals. Individuals bearing MHC allele Q show significantly reduced risks of death, and I detect positive selection along the evolutionary lineage leading to allele Q. Further, in one Bd resistant population, I detect a significant signal of directional selection for allele Q. For lab-infected frogs only, MHC heterozygotes also have a significantly reduced risk of death. In summary, I find that population genetic and immunogenetic variation contributes to Bd susceptibility after controlling for environmental variation, demonstrating that host genetics significantly affect chytridiomycosis outcomes and may be a powerful tool for conserving global amphibian biodiversity. v Advisors/Committee Members: Zamudio, Kelly (chair), Harrison, Richard Gerald (committee member), Schat, Karel Antoni (committee member).

Subjects/Keywords: amphibian; major histocompatibility complex; molecular evolution

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Savage, A. (2012). Immunogenetic Adaptation To An Emergent Amphibian Disease. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/29197

Chicago Manual of Style (16^th Edition):

Savage, Anna. “Immunogenetic Adaptation To An Emergent Amphibian Disease.” 2012. Doctoral Dissertation, Cornell University. Accessed March 05, 2021. http://hdl.handle.net/1813/29197.

MLA Handbook (7^th Edition):

Savage, Anna. “Immunogenetic Adaptation To An Emergent Amphibian Disease.” 2012. Web. 05 Mar 2021.

Vancouver:

Savage A. Immunogenetic Adaptation To An Emergent Amphibian Disease. [Internet] [Doctoral dissertation]. Cornell University; 2012. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1813/29197.

Council of Science Editors:

Savage A. Immunogenetic Adaptation To An Emergent Amphibian Disease. [Doctoral Dissertation]. Cornell University; 2012. Available from: http://hdl.handle.net/1813/29197

California State University – Northridge

30. Dimashkie, Anupama Reddy Sadhu. Epigenetic barriers to X chromosome reactivation during reprogramming to induced pluripotency & molecular evolution of myb genes in Hawaiian Silverswords and California Tarweeds.

Degree: MS, Biology, 2013, California State University – Northridge

URL: http://hdl.handle.net/10211.2/3434

► The differentiated state of somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs), leading to the reactivation of the inactive X chromosome (Xi)… (more)

▼ The differentiated state of somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs), leading to the reactivation of the inactive X chromosome (Xi) of female differentiated cells in the mouse. In somatic cells, the Xi is very stable however, when reprogramming mouse embryonic fibroblasts, the Xi reactivates upon completion to a pluripotent state. How somatic character is reversed as well as the sequence of epigenetic events leading to X chromosome reactivation during reprogramming to iPSCs, is not well understood. We found that, the non-coding RNA Xist and DNA methylation are present on the Xi in clonal late reprogramming intermediates, pre-iPSCs, suggesting that these are reversed late during reprogramming. To test whether these function in maintaining Xi repression at this stage of reprogramming we functionally interfered with Xist and DNA methylation using pre-iPSCs genetically deleted for Xist and/or treated with siDNMT1 (DNA methyltransferase 1) and DNA methyltransferase inhibitor 5AzadC (5-aza-2'-deoxycytidine). Reactivation of the X chromosome occurs upon deletion of Xist and both treatments. We used bisulfite sequencing to confirm the loss of DNA methylation of X-linked genes in pre-iPSC and found the loss of DNA methylation on the Xi occurs in the presence or absence of Xist with both 5AzadC and siDNMT1. This suggests DNA demethylation is a late event in Xi reactivation and occurs very late in reprogramming. To further test this, we purified the SSEA1+ population directly from a reprogramming culture that represents a state where the pluripotency marker Nanog is already active but the Xi is not yet reactivated. We show from these intermediates that the promoter region of Nanog is demethylated. However, promoter regions of Xi-linked genes from these intermediates are still completely methylated. Together, our results identify new late stages of reprogramming to iPSCs. Advisors/Committee Members: Oberholzer Vandergon, Virginia M. (advisor), Malone, Cindy (committee member).

Subjects/Keywords: Molecular evolution; Dissertations, Academic – CSUN – Biology.

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dimashkie, A. R. S. (2013). Epigenetic barriers to X chromosome reactivation during reprogramming to induced pluripotency & molecular evolution of myb genes in Hawaiian Silverswords and California Tarweeds. (Masters Thesis). California State University – Northridge. Retrieved from http://hdl.handle.net/10211.2/3434

Chicago Manual of Style (16^th Edition):

Dimashkie, Anupama Reddy Sadhu. “Epigenetic barriers to X chromosome reactivation during reprogramming to induced pluripotency & molecular evolution of myb genes in Hawaiian Silverswords and California Tarweeds.” 2013. Masters Thesis, California State University – Northridge. Accessed March 05, 2021. http://hdl.handle.net/10211.2/3434.

MLA Handbook (7^th Edition):

Dimashkie, Anupama Reddy Sadhu. “Epigenetic barriers to X chromosome reactivation during reprogramming to induced pluripotency & molecular evolution of myb genes in Hawaiian Silverswords and California Tarweeds.” 2013. Web. 05 Mar 2021.

Vancouver:

Dimashkie ARS. Epigenetic barriers to X chromosome reactivation during reprogramming to induced pluripotency & molecular evolution of myb genes in Hawaiian Silverswords and California Tarweeds. [Internet] [Masters thesis]. California State University – Northridge; 2013. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10211.2/3434.

Council of Science Editors:

Dimashkie ARS. Epigenetic barriers to X chromosome reactivation during reprogramming to induced pluripotency & molecular evolution of myb genes in Hawaiian Silverswords and California Tarweeds. [Masters Thesis]. California State University – Northridge; 2013. Available from: http://hdl.handle.net/10211.2/3434

		in
And / Or
		in
And / Or
		in
And / Or
		in

Open Access Theses and Dissertations